286 results on '"Philip A. Lewis"'
Search Results
2. Evidence of abnormality in glutathione metabolism in the airways of preterm born children with a history of bronchopulmonary dysplasia
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Christopher W. Course, Philip A. Lewis, Sarah J. Kotecha, Michael Cousins, Kylie Hart, Kate J. Heesom, W. John Watkins, and Sailesh Kotecha
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Medicine ,Science - Abstract
Abstract Preterm-born children are at risk of long-term pulmonary deficits, including those who developed bronchopulmonary dysplasia (BPD) in infancy, however the underlying mechanisms remain poorly understood. We characterised the exhaled breath condensate (EBC) metabolome from preterm-born children, both with and without BPD. Following spirometry, EBC from children aged 7–12 years, from the Respiratory Health Outcomes in Neonates study, were analysed using Time-of-Flight Mass Spectrometry. Metabolite Set Enrichment Analysis (MSEA) linked significantly altered metabolites to biological processes. Linear regression models examined relationships between metabolites of interest and participant demographics. EBC was analysed from 214 children, 144 were born preterm, including 34 with BPD. 235 metabolites were detected, with 38 above the detection limit in every sample. Alanine and pyroglutamic acid were significantly reduced in the BPD group when compared to preterm controls. MSEA demonstrated a reduction in glutathione metabolism. Reduced quantities of alanine, ornithine and urea in the BPD group were linked with alteration of the urea cycle. Linear regression revealed significant associations with BPD when other characteristics were considered, but not with current lung function parameters. In this exploratory study of the airway metabolome, preterm-born children with a history of BPD had changes consistent with reduced antioxidant mechanisms suggesting oxidative stress.
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- 2023
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3. Multi-omic approach characterises the neuroprotective role of retromer in regulating lysosomal health
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James L. Daly, Chris M. Danson, Philip A. Lewis, Lu Zhao, Sara Riccardo, Lucio Di Filippo, Davide Cacchiarelli, Daehoon Lee, Stephen J. Cross, Kate J. Heesom, Wen-Cheng Xiong, Andrea Ballabio, James R. Edgar, and Peter J. Cullen
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Science - Abstract
Abstract Retromer controls cellular homeostasis through regulating integral membrane protein sorting and transport and by controlling maturation of the endo-lysosomal network. Retromer dysfunction, which is linked to neurodegenerative disorders including Parkinson’s and Alzheimer’s diseases, manifests in complex cellular phenotypes, though the precise nature of this dysfunction, and its relation to neurodegeneration, remain unclear. Here, we perform an integrated multi-omics approach to provide precise insight into the impact of Retromer dysfunction on endo-lysosomal health and homeostasis within a human neuroglioma cell model. We quantify widespread changes to the lysosomal proteome, indicative of broad lysosomal dysfunction and inefficient autophagic lysosome reformation, coupled with a reconfigured cell surface proteome and secretome reflective of increased lysosomal exocytosis. Through this global proteomic approach and parallel transcriptomic analysis, we provide a holistic view of Retromer function in regulating lysosomal homeostasis and emphasise its role in neuroprotection.
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- 2023
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4. Modulation of pulmonary desmosomes by inhaler therapy in preterm-born children with bronchopulmonary dysplasia
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Christopher W. Course, Philip A. Lewis, Sarah J. Kotecha, Michael Cousins, Kylie Hart, W. John Watkins, Kate J. Heesom, and Sailesh Kotecha
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Medicine ,Science - Abstract
Abstract Despite evidence demonstrating persistent lung function deficits in preterm-born children, especially in those who had bronchopulmonary dysplasia (BPD) in infancy, the underlying biological mechanisms explaining these lung function deficits remain poorly understood. We characterised the exhaled breath condensate (EBC) proteome in preterm-born children, with and without BPD; and before and after inhaler treatment. EBC from children aged 7–12 years, from the Respiratory Health Outcomes in Neonates (RHiNO) study, were analysed by Nano-LC Mass Spectrometry with Tandem Mass Tag labelling. Children with percent predicted forced expiratory volume in 1 second ≤ 85% were enrolled to a 12-week blinded randomised trial of inhaled corticosteroids alone (ICS) or with long-acting β2-agonist (ICS/LABA) or placebo. EBC was analysed from 218 children at baseline, and 46 children received randomised inhaled therapy. 210 proteins were detected in total. For the 19 proteins present in every sample, the desmosome proteins: desmoglein-1, desmocollin-1 and plakoglobin were significantly decreased, and cytokeratin-6A was increased in preterm-born children with BPD when compared to preterm- and term-born controls. ICS/LABA treatment significantly increased abundance of desmoglein-1, desmocollin-1 and plakoglobin in the BPD group with low lung function, and significantly increased plakoglobin in those without BPD. No differences were noted after ICS treatment. Exploratory analyses of proteins not detected in all samples suggested decreased abundance of several antiproteases. This study provides proteomic evidence of ongoing pulmonary structural changes with decreased desmosomes in school-aged preterm-born children with BPD and low lung function, which was reversed with combined inhaled corticosteroids and long-acting β2-agonists therapy.
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- 2023
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5. SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription
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Abdulaziz Almuqrin, Andrew D. Davidson, Maia Kavanagh Williamson, Philip A. Lewis, Kate J. Heesom, Susan Morris, Sarah C. Gilbert, and David A. Matthews
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Medicine ,Genetics ,QH426-470 - Abstract
Abstract Background ChAdOx1 nCoV-19 is a recombinant adenovirus vaccine against SARS-CoV-2 that has passed phase III clinical trials and is now in use across the globe. Although replication-defective in normal cells, 28 kbp of adenovirus genes is delivered to the cell nucleus alongside the SARS-CoV-2 S glycoprotein gene. Methods We used direct RNA sequencing to analyse transcript expression from the ChAdOx1 nCoV-19 genome in human MRC-5 and A549 cell lines that are non-permissive for vector replication alongside the replication permissive cell line, HEK293. In addition, we used quantitative proteomics to study over time the proteome and phosphoproteome of A549 and MRC5 cells infected with the ChAdOx1 nCoV-19 vaccine. Results The expected SARS-CoV-2 S coding transcript dominated in all cell lines. We also detected rare S transcripts with aberrant splice patterns or polyadenylation site usage. Adenovirus vector transcripts were almost absent in MRC-5 cells, but in A549 cells, there was a broader repertoire of adenoviral gene expression at very low levels. Proteomically, in addition to S glycoprotein, we detected multiple adenovirus proteins in A549 cells compared to just one in MRC5 cells. Conclusions Overall, the ChAdOx1 nCoV-19 vaccine’s transcriptomic and proteomic repertoire in cell culture is as expected. The combined transcriptomic and proteomics approaches provide a detailed insight into the behaviour of this important class of vaccine using state-of-the-art techniques and illustrate the potential of this technique to inform future viral vaccine vector design.
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- 2021
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6. Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein
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Andrew D. Davidson, Maia Kavanagh Williamson, Sebastian Lewis, Deborah Shoemark, Miles W. Carroll, Kate J. Heesom, Maria Zambon, Joanna Ellis, Philip A. Lewis, Julian A. Hiscox, and David A. Matthews
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Medicine ,Genetics ,QH426-470 - Abstract
Abstract Background SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this novel coronavirus to provide a fundamental description of the virus’s genomic and proteomic potential. Methods We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. Allied to this, we used tandem mass spectrometry to investigate the proteome and phosphoproteome of the same virally infected cells. Results Our integrated analysis revealed that the viral transcripts (i.e. subgenomic mRNAs) generally fitted the expected transcription model for coronaviruses. Importantly, a 24 nt in-frame deletion was detected in over half of the subgenomic mRNAs encoding the spike (S) glycoprotein and was predicted to remove a proposed furin cleavage site from the S glycoprotein. Tandem mass spectrometry identified over 500 viral peptides and 44 phosphopeptides in virus-infected cells, covering almost all proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. Conclusions Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein, a leading vaccine target, shows that this and other regions of SARS-CoV-2 proteins may readily mutate. The furin site directs cleavage of the S glycoprotein into functional subunits during virus entry or exit and likely contributes strongly to the pathogenesis and zoonosis of this virus. Our data emphasises that the viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.
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- 2020
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7. Accounting Offshoring: The role of Emotional Intelligence
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Gaurav Gupta, Stephen B. Salter, and Philip A. Lewis
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India ,emotional intelligence ,audit ,culture ,offshoring ,Big 4 accounting firms ,Business ,HF5001-6182 ,Accounting. Bookkeeping ,HF5601-5689 - Abstract
Research Question: The primary purposes of this paper are to compare the emotional intelligence levels of Americans and Indians and explore the potential impacts of these differences in the offshoring relationships. Motivation: The continued growth of the Indian economy and its legions of inexpensive English-speaking graduates has made India a global leader in business process offshoring. U.S. companies, including accounting firms, routinely offshore a variety of their business functions to India. However, the effective functioning of these offshoring relationships has been offset by perceptions of the Indian providers’ poor communication and ineffective management training (Downey, 2018; Jain, 2015; Mayur, James, and Swamynathan, 2015). We believe that a culture-influenced behavioral factor known as Emotional Intelligence (EI) has resulted in less than the optimal performance outcome for the U.S. public accounting firms in these offshoring relationships. Data: Using MSCEIT EI inventory, we collect data from 197 master’s students enrolled in accounting courses in India and the U.S. on four branches of EI. Findings: Our results indicate that the Indian students have statistically lower levels of EI than the U.S. students. We discuss the implications for public accounting firms that offshore to India and advocate for the inclusion of the EI related coursework in Indian master’s programs and firm training. Contribution: Using a well-established inventory of EI, our study provides a deeper understanding of the cultural EI differences between Americans and Indians, and the possible implications for the offshoring environment.
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- 2019
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8. The type 2 diabetes gene product STARD10 is a phosphoinositide-binding protein that controls insulin secretory granule biogenesis
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Gaelle R. Carrat, Elizabeth Haythorne, Alejandra Tomas, Leena Haataja, Andreas Müller, Peter Arvan, Alexandra Piunti, Kaiying Cheng, Mutian Huang, Timothy J. Pullen, Eleni Georgiadou, Theodoros Stylianides, Nur Shabrina Amirruddin, Victoria Salem, Walter Distaso, Andrew Cakebread, Kate J. Heesom, Philip A. Lewis, David J. Hodson, Linford J. Briant, Annie C.H. Fung, Richard B. Sessions, Fabien Alpy, Alice P.S. Kong, Peter I. Benke, Federico Torta, Adrian Kee Keong Teo, Isabelle Leclerc, Michele Solimena, Dale B. Wigley, and Guy A. Rutter
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Type 2 diabetes ,Pancreatic β-cell ,Lipid transporter ,Insulin granule biogenesis ,Phosphoinositides ,Internal medicine ,RC31-1245 - Abstract
Objective: Risk alleles for type 2 diabetes at the STARD10 locus are associated with lowered STARD10 expression in the β-cell, impaired glucose-induced insulin secretion, and decreased circulating proinsulin:insulin ratios. Although likely to serve as a mediator of intracellular lipid transfer, the identity of the transported lipids and thus the pathways through which STARD10 regulates β-cell function are not understood. The aim of this study was to identify the lipids transported and affected by STARD10 in the β-cell and the role of the protein in controlling proinsulin processing and insulin granule biogenesis and maturation. Methods: We used isolated islets from mice deleted selectively in the β-cell for Stard10 (βStard10KO) and performed electron microscopy, pulse-chase, RNA sequencing, and lipidomic analyses. Proteomic analysis of STARD10 binding partners was executed in the INS1 (832/13) cell line. X-ray crystallography followed by molecular docking and lipid overlay assay was performed on purified STARD10 protein. Results: βStard10KO islets had a sharply altered dense core granule appearance, with a dramatic increase in the number of “rod-like” dense cores. Correspondingly, basal secretion of proinsulin was increased versus wild-type islets. The solution of the crystal structure of STARD10 to 2.3 Å resolution revealed a binding pocket capable of accommodating polyphosphoinositides, and STARD10 was shown to bind to inositides phosphorylated at the 3’ position. Lipidomic analysis of βStard10KO islets demonstrated changes in phosphatidylinositol levels, and the inositol lipid kinase PIP4K2C was identified as a STARD10 binding partner. Also consistent with roles for STARD10 in phosphoinositide signalling, the phosphoinositide-binding proteins Pirt and Synaptotagmin 1 were amongst the differentially expressed genes in βStard10KO islets. Conclusion: Our data indicate that STARD10 binds to, and may transport, phosphatidylinositides, influencing membrane lipid composition, insulin granule biosynthesis, and insulin processing.
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- 2020
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9. High quality clinical grade human embryonic stem cell lines derived from fresh discarded embryos
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Jinpei Ye, Nicola Bates, Despina Soteriou, Lisa Grady, Clare Edmond, Alex Ross, Alan Kerby, Philip A. Lewis, Tope Adeniyi, Ronnie Wright, Kay V. Poulton, Marcus Lowe, Susan J. Kimber, and Daniel R. Brison
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Embryo ,Human embryonic stem cells ,Good Manufacturing Practice ,Pluripotency ,Medicine (General) ,R5-920 ,Biochemistry ,QD415-436 - Abstract
Abstract Background Human embryonic stem cells (hESCs) hold tremendous promise for cell replacement therapies for a range of degenerative diseases. In order to provide cost-effective treatments affordable by public health systems, HLA-matched allogeneic tissue banks of the highest quality clinical-grade hESCs will be required. However only a small number of existing hESC lines are suitable for clinical use; they are limited by moral and ethical concerns and none of them apply Good Manufacturing Practice (GMP) standards to the earliest and critical stages of gamete and embryo procurement. We thus aimed to derive new clinical grade hESC lines of highest quality from fresh surplus GMP grade human embryos. Methods A comprehensive screen was performed for suitable combinations of culture media with supporting feeder cells or feeder-free matrix, at different stages, to support expansion of the inner cell mass and to establish new hESC lines. Results We developed a novel two-step and sequential media system of clinical-grade hESC derivation and successfully generated seven new hESC lines of widely varying HLA type, carefully screened for genetic health, from human embryos donated under the highest ethical and moral standards under an integrated GMP system which extends from hESC banking all the way back to gamete and embryo procurement. Conclusions The present study, for the first time, reports the successful derivation of highest-quality clinical-grade hESC lines from fresh poor-quality surplus human embryos generated in a GMP-grade IVF laboratory. The availability of hESC lines of this status represents an important step towards more widespread application of regenerative medicine therapies.
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- 2017
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10. An Investigation into Design of Blood Pressure Cuffs Using the Tekscan Pressure Sensing System
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Shenela Naqvi, Muhammad Amir, Farhana Naeem, Tilak Dias, and Philip S. Lewis
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Polymers and Plastics ,Process Chemistry and Technology ,Materials Chemistry - Abstract
Cuff design is the most important aspect to work on for the accurate measurement of blood pressure. For the very first time, pressure distribution underneath different parts/components of the fabric cuffs was analysed in detail using an advanced interface pressure sensing system. The pressure distribution at the interface of the selected cuffs and an arm simulator were measured experimentally while simulating blood pressure measurement. Fabrics are the main cuff constructing material and a relationship was found between cuff fabric properties and pressure at the interface of the cuff and the arm simulator. It was also found that the pressure distribution under different parts of the same cuff varied due to the uneven contact of the cuff fabric with the arm simulator. Components attached to cuff fabric which facilitate blood pressure measurement either confine or drive fabric according to their size and placement; they may cause non-uniform interface pressure distribution on the human arm too. It was also examined whether the selected cuffs were applying higher or lower average pressure over the surface of the simulator and the range varied from 8 mmHg to 25 mmHg. This indicates that the subsequent pressure distribution inside the arm tissues and over an artery would also vary further due to the cuffs being of different designs. This study found that cuffs would be unable to transfer the required pressure over the artery to block blood flow as and when needed.
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- 2022
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11. Restoration of vision using wireless cortical implants: The Monash Vision Group project.
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Arthur James Lowery, Jeffrey V. Rosenfeld, Philip M. Lewis, Damien Browne, Anand Mohan, Emma Brunton, Edwin Yan, Jerome J. Maller, Collette Mann, Ramesh Rajan, Marcello Rosa, and Jeanette Pritchard
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- 2015
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12. Novel Collagen Surgical Patches for Local Delivery of Multiple Drugs
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Xiao Liu, Marius Berthel, Grishmi Rajbhandari, Ying Zhou, Philip M. Lewis, Zhilian Yue, and Gordon G. Wallace
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Drug Discovery ,Pharmaceutical Science ,Molecular Medicine - Published
- 2023
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13. Hypoxia shapes the immune landscape in lung injury and promotes the persistence of inflammation
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Ananda S. Mirchandani, Stephen J. Jenkins, Calum C. Bain, Manuel A. Sanchez-Garcia, Hannah Lawson, Patricia Coelho, Fiona Murphy, David M. Griffith, Ailiang Zhang, Tyler Morrison, Tony Ly, Simone Arienti, Pranvera Sadiku, Emily R. Watts, Rebecca. S. Dickinson, Leila Reyes, George Cooper, Sarah Clark, David Lewis, Van Kelly, Christos Spanos, Kathryn M. Musgrave, Liam Delaney, Isla Harper, Jonathan Scott, Nicholas J. Parkinson, Anthony J. Rostron, J. Kenneth Baillie, Sara Clohisey, Clare Pridans, Lara Campana, Philip Starkey Lewis, A. John Simpson, David H. Dockrell, Jürgen Schwarze, Nikhil Hirani, Peter J. Ratcliffe, Christopher W. Pugh, Kamil Kranc, Stuart J. Forbes, Moira K. B. Whyte, and Sarah R. Walmsley
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Inflammation ,Respiratory Distress Syndrome ,Immunology ,Lung Injury ,Cell Biology ,Biochemistry & Proteomics ,Mice ,Signalling & Oncogenes ,Metabolism ,Animals ,Humans ,Immunology and Allergy ,Hypoxia ,Lung - Abstract
Hypoxemia is a defining feature of acute respiratory distress syndrome (ARDS), an often-fatal complication of pulmonary or systemic inflammation, yet the resulting tissue hypoxia, and its impact on immune responses, is often neglected. In the present study, we have shown that ARDS patients were hypoxemic and monocytopenic within the first 48 h of ventilation. Monocytopenia was also observed in mouse models of hypoxic acute lung injury, in which hypoxemia drove the suppression of type I interferon signaling in the bone marrow. This impaired monopoiesis resulted in reduced accumulation of monocyte-derived macrophages and enhanced neutrophil-mediated inflammation in the lung. Administration of colony-stimulating factor 1 in mice with hypoxic lung injury rescued the monocytopenia, altered the phenotype of circulating monocytes, increased monocyte-derived macrophages in the lung and limited injury. Thus, tissue hypoxia altered the dynamics of the immune response to the detriment of the host and interventions to address the aberrant response offer new therapeutic strategies for ARDS.
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- 2022
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14. SNAPSHOT Isolation: Why Do Some People Call it SERIALIZABLE?
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Philip M. Lewis
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- 2013
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15. Attributed Translations.
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Philip M. Lewis, Daniel J. Rosenkrantz, and Richard Edwin Stearns
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- 2013
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16. Consistency and serializability in concurrent database systems.
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Daniel J. Rosenkrantz, Richard Edwin Stearns, and Philip M. Lewis
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- 2013
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17. System Level Concurrency Control for Distributed Database Systems.
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Daniel J. Rosenkrantz, Richard Edwin Stearns, and Philip M. Lewis
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- 2013
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18. An analysis of several heuristics for the traveling salesman problem.
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Daniel J. Rosenkrantz, Richard Edwin Stearns, and Philip M. Lewis
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- 2013
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19. Multiomic Approach Characterises the Neuroprotective Role of Retromer in Regulating Lysosomal Health
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James L. Daly, Chris M. Danson, Philip A. Lewis, Sara Riccardo, Lucio Di Filippo, Davide Cacchiarelli, Stephen J. Cross, Kate J. Heesom, Andrea Ballabio, James R. Edgar, and Peter J. Cullen
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Retromer controls cellular homeostasis through regulating integral membrane protein sorting and transport and by controlling late-stage maturation of the endo-lysosomal network. Retromer dysfunction, which is linked to neurodegenerative disorders including Parkinson’s and Alzheimer’s diseases, manifests in complex cellular phenotypes, though the precise nature of this dysfunction, and its relation to neurodegeneration, remain unclear. Here, we perform the first integrated multiomics approach to provide precise insight into the impact of Retromer dysfunction on endo-lysosomal health and homeostasis within a human neuroglioma cell model. We quantify profound changes to the lysosomal proteome, indicative of broad lysosomal dysfunction and inefficient autophagic lysosome reformation, coupled with a reconfigured cell surface proteome and secretome reflective of increased lysosomal exocytosis. Through this global proteomic approach and parallel transcriptomic analysis, we provide an unprecedented integrated view of Retromer function in regulating lysosomal homeostasis and emphasise its role in neuroprotection.
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- 2022
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20. An Azobenzene G-quadruplex Ligand Exhibits Promising Antibacterial Activity against Escherichia coli
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Javier Ramos-Soriano, Yuiko Takebayashi, Jenny Samphire, Michael P. O’Hagan, Catherine Gurr, Kate J. Heesom, Philip A. Lewis, James Spencer, and M. Carmen Galan
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With the rise in bacterial antimicrobial resistance (AMR) and decline in antibiotic discovery, global healthcare is at a point of jeopardy. There is great need for the development of novel antimicrobials that target bacteria that have become resistant to our existing antibiotics, in particular Gram-negative species such as Escherichia coli which is responsible for opportunistic infections of already compromised patients. Here we demonstrate that a novel pyridinium-functionalised azobenzene scaffold L20, identified as a candidate ligand able target G-quadruplex (G4) structures in bacterial genomes/transcriptomes, shows promising antibacterial activity (MIC values ≤ 4 µg/ml) against multi-drug resistant E. coli. Tandem Mass Tag (TMT) proteomics applied to cultures of the E. coli type strain ATCC 25922 treated with sub-lethal concentrations of L20, identified seven G4-containing sequences as potential targets for L20. FRET (fluorescence resonance energy transfer) stabilisation assays indicate L20 binds these selected sequences with variable and moderate affinity, in contrast to two comparator G4 ligands (stiff-stilbene L5 and pyridostatin (PDS)) that better stabilise G4 structures but exhibit a lower antimicrobial activity. However, proteomic experiments also reveal that, alongside its superior antibacterial activity, L20 treatment influences expression levels of more G4-associated proteins than either L5 or PDS, and upregulates multiple essential proteins involved in translation. These findings identify strategies discovering potential G4 ligands as approaches that can lead to antibacterial candidates active against priority targets such as multi-drug resistant E. coli, and that targeting G4 sequences, and ligands such as L20, warrant further exploration as potential novel therapeutics with G4-mediated modes of action.
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- 2022
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21. Location, biophysical and agronomic parameters for croplands in Northern Ghana
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Jose Luis Gómez-Dans, Philip Edward Lewis, Feng Yin, Kofi Asare, Patrick Lamptey, Kenneth Kobina Yedu Aidoo, Dilys MacCarthy, Hongyuan Ma, Qingling Wu, Martin Addi, Stephen Aboagye-Ntow, Caroline Edinam Doe, Rahaman Alhassan, Isaac Kankam-Boadu, Jianxi Huang, and Xuecao Li
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General Earth and Planetary Sciences - Abstract
Smallholder agriculture is the bedrock of the food production system in sub-Saharan Africa. Yields in Africa are significantly below potentially attainable yields for a number of reasons, and they are particularly vulnerable to climate change impacts. Monitoring of these highly heterogeneous landscapes is needed to respond to farmer needs, develop an appropriate policy and ensure food security, and Earth observation (EO) must be part of these efforts, but there is a lack of ground data for developing and testing EO methods in western Africa, and in this paper, we present data on (i) crop locations, (ii) biophysical parameters and (iii) crop yield, and biomass was collected in 2020 and 2021 in Ghana and is reported in this paper. In 2020, crop type was surveyed in more than 1800 fields in three different agroecological zones across Ghana (the Guinea Savannah, Transition and Deciduous zones). In 2021, a smaller number of fields were surveyed in the Guinea Savannah zone, and additionally, repeated measurements of leaf area index (LAI) and leaf chlorophyll concentration were made on a set of 56 maize fields. Yield and biomass were also sampled at harvesting. LAI in the sampled fields ranged from 0.1 to 5.24 m2 m−2, whereas leaf chlorophyll concentration varied between 6.1 and 60.3 µg cm−2. Yield varied between 190 and 4580 kg ha−1, with an important within-field variability (average per-field standard deviation 381 kg ha−1). The data are used in this paper to (i) evaluate the Digital Earth Africa 2019 cropland masks, where 61 % of sampled 2020/21 cropland is flagged as cropland by the data set, (ii) develop and test an LAI retrieval method from Earth observation Planet surface reflectance data (validation correlation coefficient R=0.49, root mean square error (RMSE) 0.44 m2 m−2), (iii) create a maize classification data set for Ghana for 2021 (overall accuracy within the region tested: 0.84), and (iv) explore the relationship between maximum LAI and crop yield using a linear model (correlation coefficient R=0.66 and R=0.53 for in situ and Planet-derived LAI, respectively). The data set, made available here within the context of the Group on Earth Observations Global Agricultural Monitoring (GEOGLAM) initiative, is an important contribution to understanding crop evolution and distribution in smallholder farming systems and will be useful for researchers developing/validating methods to monitor these systems using Earth observation data. The data described in this paper are available from https://doi.org/10.5281/zenodo.6632083 (Gomez-Dans et al., 2022).
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- 2022
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22. Experimental investigation on pressure transmission underneath blood pressure cuffs of different types using an arm simulator
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Prasad Potluri, Philip S. Lewis, Shenela Naqvi, and Parthasarathi Mandal
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010407 polymers ,Pressure transmission ,Blood pressure cuffs ,Materials science ,Blood pressure ,Polymers and Plastics ,Materials Science (miscellaneous) ,General Agricultural and Biological Sciences ,01 natural sciences ,Industrial and Manufacturing Engineering ,0104 chemical sciences ,Biomedical engineering - Abstract
Thirty-seven blood pressure cuffs constructed with different fabrics, grouped into eight structural sub-types, are selected to investigate their relative effects on potential measurements of blood ...
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- 2021
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23. SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription
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Maia Kavanagh Williamson, Abdulaziz Almuqrin, Andrew D. Davidson, Sarah C. Gilbert, David A. Matthews, Philip A. Lewis, Susan J. Morris, and Kate J. Heesom
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Proteomics ,COVID-19 Vaccines ,Transcription, Genetic ,lcsh:QH426-470 ,Gene Expression ,lcsh:Medicine ,Biology ,Polyadenylation ,Cell Line ,Viral vector ,Genetics ,medicine ,Humans ,RNA, Messenger ,Molecular Biology ,Gene ,Cells, Cultured ,Genetics (clinical) ,Regulation of gene expression ,SARS-CoV-2 ,Research ,Gene Expression Profiling ,Viral Vaccine ,HEK 293 cells ,lcsh:R ,COVID-19 ,Covid19 ,Virology ,Adenovirus vaccine ,Gene expression profiling ,lcsh:Genetics ,Gene Expression Regulation ,Cell culture ,Host-Pathogen Interactions ,Spike Glycoprotein, Coronavirus ,RNA, Viral ,Molecular Medicine ,medicine.drug - Abstract
Background ChAdOx1 nCoV-19 is a recombinant adenovirus vaccine against SARS-CoV-2 that has passed phase III clinical trials and is now in use across the globe. Although replication-defective in normal cells, 28 kbp of adenovirus genes is delivered to the cell nucleus alongside the SARS-CoV-2 S glycoprotein gene. Methods We used direct RNA sequencing to analyse transcript expression from the ChAdOx1 nCoV-19 genome in human MRC-5 and A549 cell lines that are non-permissive for vector replication alongside the replication permissive cell line, HEK293. In addition, we used quantitative proteomics to study over time the proteome and phosphoproteome of A549 and MRC5 cells infected with the ChAdOx1 nCoV-19 vaccine. Results The expected SARS-CoV-2 S coding transcript dominated in all cell lines. We also detected rare S transcripts with aberrant splice patterns or polyadenylation site usage. Adenovirus vector transcripts were almost absent in MRC-5 cells, but in A549 cells, there was a broader repertoire of adenoviral gene expression at very low levels. Proteomically, in addition to S glycoprotein, we detected multiple adenovirus proteins in A549 cells compared to just one in MRC5 cells. Conclusions Overall, the ChAdOx1 nCoV-19 vaccine’s transcriptomic and proteomic repertoire in cell culture is as expected. The combined transcriptomic and proteomics approaches provide a detailed insight into the behaviour of this important class of vaccine using state-of-the-art techniques and illustrate the potential of this technique to inform future viral vaccine vector design.
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- 2021
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24. Semantics Based Verification and Synthesis of BPEL4WS Abstract Processes.
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Ziyang Duan, Arthur J. Bernstein, Philip M. Lewis, and Shiyong Lu
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- 2004
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25. A model for abstract process specification, verification and composition.
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Ziyang Duan, Arthur J. Bernstein, Philip M. Lewis, and Shiyong Lu
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- 2004
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26. Extracellular matrix and vascular dynamics in the kidney of a murine model for Marfan syndrome
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Rodrigo Barbosa de Souza, Renan Barbosa Lemes, Orestes Foresto-Neto, Luara Lucena Cassiano, Dieter P. Reinhardt, Keith M. Meek, Ivan Hong Jun Koh, Philip N. Lewis, and Lygia V. Pereira
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Multidisciplinary - Abstract
Fibrillin-1 is a pivotal structural component of the kidney’s glomerulus and peritubular tissue. Mutations in the fibrillin-1 gene result in Marfan syndrome (MFS), an autosomal dominant disease of the connective tissue. Although the kidney is not considered a classically affected organ in MFS, several case reports describe glomerular disease in patients. Therefore, this study aimed to characterize the kidney in the mgΔlpn-mouse model of MFS. Affected animals presented a significant reduction of glomerulus, glomerulus-capillary, and urinary space, and a significant reduction of fibrillin-1 and fibronectin in the glomerulus. Transmission electron microscopy and 3D-ultrastructure analysis revealed decreased amounts of microfibrils which also appeared fragmented in the MFS mice. Increased collagen fibers types I and III, MMP-9, and α-actin were also observed in affected animals, suggesting a tissue-remodeling process in the kidney. Video microscopy analysis showed an increase of microvessel distribution coupled with reduction of blood-flow velocity, while ultrasound flow analysis revealed significantly lower blood flow in the kidney artery and vein of the MFS mice. The structural and hemodynamic changes of the kidney indicate the presence of kidney remodeling and vascular resistance in this MFS model. Both processes are associated with hypertension which is expected to worsen the cardiovascular phenotype in MFS.
- Published
- 2023
- Full Text
- View/download PDF
27. Characterisation of carapace composition in developing and adult ostracods (Skogsbergia lerneri) and its potential for biomaterials
- Author
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Benjamin M. Rumney, Siân R. Morgan, J. Frederick W. Mosselmans, F. Tegwen Malik, Simon J. Holden, Andrew R. Parker, Nick White, Philip N. Lewis, Julie Albon, and Keith M. Meek
- Subjects
Ecology ,Aquatic Science ,Ecology, Evolution, Behavior and Systematics - Abstract
The protective carapace of Skogsbergia lerneri, a marine ostracod, is scratch-resistant and transparent. The compositional and structural organisation of the carapace that underlies these properties is unknown. In this study, we aimed to quantify and determine the distribution of chemical elements and chitin within the carapace of adult ostracods, as well as at different stages of ostracod development, to gain insight into its composition. Elemental analyses included X-ray absorption near-edge structure, X-ray fluorescence and X-ray diffraction. Nonlinear microscopy and spectral imaging were performed to determine chitin distribution within the carapace. High levels of calcium (20.3%) and substantial levels of magnesium (1.89%) were identified throughout development. Amorphous calcium carbonate (ACC) was detected in carapaces of all developmental stages, with the polymorph, aragonite, identified in A-1 and adult carapaces. Novel chitin-derived second harmonic generation signals (430/5 nm) were detected. Quantification of relative chitin content within the developing and adult carapaces identified negligible differences in chitin content between developmental stages and adult carapaces, except for the lower chitin contribution in A-2 (66.8 ± 7.6%) compared to A-5 (85.5 ± 10%) (p = 0.03). Skogsbergia lerneri carapace calcium carbonate composition was distinct to other myodocopid ostracods. These calcium polymorphs and ACC are described in other biological transparent materials, and with the consistent chitin distribution throughout S. lerneri development, may imply a biological adaptation to preserve carapace physical properties. Realisation of S. lerneri carapace synthesis and structural organisation will enable exploitation to manufacture biomaterials and biomimetics with huge potential in industrial and military applications.
- Published
- 2022
28. Hypoxia shapes the immune landscape in lung injury promoting inflammation persistence
- Author
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Ananda S. Mirchandani, Stephen J. Jenkins, Calum C. Bain, Hannah Lawson, Patricia Coelho, Fiona Murphy, David Griffith, Ailiang Zhang, Manuel A. Sanchez-Garcia, Leila Reyes, Tyler Morrison, Simone Arienti, Pranvera Sadiku, Emily R. Watts, Rebecca. S. Dickinson, Sarah Clark, Tony Ly, David Lewis, Van Kelly, Christos Spanos, Kathryn M. Musgrave, Liam Delaney, Isla Harper, Jonathan Scott, Nicholas J. Parkinson, Anthony J. Rostron, Kenneth J Baillie, Sara Clohisey, Clare Pridans, Lara Campana, Philip Starkey-Lewis, A John Simpson, David Dockrell, Jurgen Schwarze, Nikhil Hirani, Peter J. Ratcliffe, Christopher W. Pugh, Kamil Kranc, Stuart J. Forbes, Moira K. Whyte, and Sarah R. Walmsley
- Subjects
respiratory system ,respiratory tract diseases - Abstract
Acute Respiratory Distress Syndrome (ARDS), an often-fatal complication of pulmonary or systemic inflammation, has no cure. Hypoxemia is a defining feature, yet its impact on inflammation is often neglected. Patients with ARDS are monocytopenic early in the onset of the disease. Endotoxin or Streptococcus pneumoniae acute lung injury (ALI) in the context of hypoxia replicates this finding, through hypoxia-driven suppression of type I interferon signalling. This results in failed lung monocyte-derived interstitial macrophages (IM) niche expansion and unchecked neutrophilic inflammation. Administration of colony stimulating factor 1 (CSF1) rescues the monocytopenia, alters the circulating classical monocyte phenotype in hypoxic endotoxin-driven ALI and enables lung IM population expansion, thus limiting lung injury in endotoxin- and virally-induced hypoxic ALI. Hypoxia directly alters immune dynamics to the detriment of the host and manipulation of this aberrant response offers new therapeutic strategies for ARDS.
- Published
- 2022
- Full Text
- View/download PDF
29. Laser Sintering Approaches for Bone Tissue Engineering
- Author
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Jeremy N. DiNoro, Naomi C. Paxton, Jacob Skewes, Zhilian Yue, Philip M. Lewis, Robert G. Thompson, Stephen Beirne, Maria A. Woodruff, and Gordon G. Wallace
- Subjects
Polymers and Plastics ,General Chemistry - Abstract
The adoption of additive manufacturing (AM) techniques into the medical space has revolutionised tissue engineering. Depending upon the tissue type, specific AM approaches are capable of closely matching the physical and biological tissue attributes, to guide tissue regeneration. For hard tissue such as bone, powder bed fusion (PBF) techniques have significant potential, as they are capable of fabricating materials that can match the mechanical requirements necessary to maintain bone functionality and support regeneration. This review focuses on the PBF techniques that utilize laser sintering for creating scaffolds for bone tissue engineering (BTE) applications. Optimal scaffold requirements are explained, ranging from material biocompatibility and bioactivity, to generating specific architectures to recapitulate the porosity, interconnectivity, and mechanical properties of native human bone. The main objective of the review is to outline the most common materials processed using PBF in the context of BTE; initially outlining the most common polymers, including polyamide, polycaprolactone, polyethylene, and polyetheretherketone. Subsequent sections investigate the use of metals and ceramics in similar systems for BTE applications. The last section explores how composite materials can be used. Within each material section, the benefits and shortcomings are outlined, including their mechanical and biological performance, as well as associated printing parameters. The framework provided can be applied to the development of new, novel materials or laser-based approaches to ultimately generate bone tissue analogues or for guiding bone regeneration.
- Published
- 2022
30. Green Fluorescent Carbon Dots as Targeting Probes for LED-Dependent Bacterial Killing
- Author
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Stephen A. Hill, M. Carmen Galan, Eilis C. Bragginton, Josephine Dorh, Philip A. Lewis, James Spencer, Neciah Dorh, Dominic Alibhai, Jennifer Samphire, Yuiko Takebayashi, Kate J. Heesom, and Nicholas A. Hill
- Subjects
biology ,Pseudomonas aeruginosa ,Chemistry ,Bacterial killing ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,medicine.disease_cause ,Antimicrobial ,biology.organism_classification ,Tandem mass tag ,01 natural sciences ,Fluorescence ,0104 chemical sciences ,3. Good health ,Antibiotic resistance ,Biochemistry ,medicine ,0210 nano-technology ,Escherichia coli ,Bacteria - Abstract
The emergence of antimicrobial resistance represents a significant health and economic challenge worldwide. The slow pace of antibacterial discovery necessitates strategies for optimal use of existing agents, including effective diagnostics able to drive informed prescribing; and development of alternative therapeutic strategies that go beyond traditional small-molecule approaches. Thus, the development of novel probes able to target bacteria for detection and killing, and that can pave the way to effective theranostic strategies, is of great importance. Here we demonstrate that metal-free green-emitting fluorescent carbon dots (FCDs) synthesized from glucosamine HCl and m-phenylenediamine, and featuring 2,5-deoxyfructosazine on a robust amorphous core, can label both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa) bacterial pathogens within 10 minutes of exposure. Moreover, effective killing of Gram-positive and -negative bacteria can be induced by combining FCD treatment with irradiation by LED light in the visible range. Cell-based, electron microscopy and Tandem Mass Tag (TMT) proteomic experiments indicate that FCD administration in combination with LED exposure gives rise to local heating, ROS production, and membrane- and DNA-damage, suggesting multiple routes to FCD-mediated bacterial killing. Our data identify FCDs as materials that combine facile synthesis from low-cost precursors with labelling and light-dependent killing of clinically important bacterial species, and that thus warrant further exploration as the potential bases for novel theranostics.
- Published
- 2022
- Full Text
- View/download PDF
31. Semantic Conditions for Correctness at Different Isolation Levels.
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Arthur J. Bernstein, Philip M. Lewis, and Shiyong Lu
- Published
- 2000
- Full Text
- View/download PDF
32. Validation of the Kinetik Blood Pressure Monitor—Series 1 for use in adults at home and in clinical settings, according to the 2002 European Society of Hypertension International Protocol on the validation of blood pressure devices
- Author
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Claire Schwartz, A Kirkham, PS Lacy, Philip S. Lewis, James P Sheppard, W Gamble, C Peers, K Edwards, P Swales, Bryan Williams, Sinead T. J. McDonagh, and J Howarth
- Subjects
Adult ,medicine.medical_specialty ,business.industry ,Diastole ,Blood Pressure ,Blood Pressure Determination ,Clinical settings ,Blood Pressure Monitoring, Ambulatory ,030204 cardiovascular system & hematology ,Sphygmomanometers ,Blood Pressure Monitors ,Mean difference ,03 medical and health sciences ,0302 clinical medicine ,Blood pressure ,Hypertension ,Internal Medicine ,Physical therapy ,Humans ,Medicine ,030212 general & internal medicine ,business - Abstract
The aim of this study was to assess the blood pressure (BP) measurement accuracy of the Kinetik Blood Pressure Monitor—Series 1 (BPM-1) for use in home or clinical settings according to the 2002 European Society of Hypertension International Protocol (ESH-IP). Forty-two participants were recruited to fulfil the required number of systolic and diastolic BP measurements according to the ESH-IP. Nine sequential same-arm BP readings were measured and analysed for each participant using the test device and observer mercury standard readings according to the 2002 ESH-IP. Forty one participants were used to obtain 33 sets of systolic and diastolic BP readings and were included in the analysis. Mean difference between the device measurements and the observer (mercury standard) measurements was 1.1 ± 7.2/1.1 ± 6.8 mmHg (mean ± standard deviation; systolic/diastolic). The number of systolic BP differences between the test and observer measurements that fell within 5, 10 and 15 mmHg was 65, 86 and 92. For diastolic readings, the number of test—observer measurement differences within 5, 10 and 15 mmHg was 77, 91 and 94. The number of participants with at least two out of three differences within 5 mmHg was 28 for systolic and 40 for diastolic BP readings. Three participants had no differences between the test and observer measurements within 5 mmHg in both the systolic and diastolic measurement categories. The Kinetik BPM-1 device fulfilled the requirements of the ESH-IP validation procedure and can be recommended for clinical use and self-measurement within the home.
- Published
- 2020
- Full Text
- View/download PDF
33. Establishment of long-term ostracod epidermal culture
- Author
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Simon Holden, Julie Albon, Siân R. Morgan, Keith M. Meek, Philip N. Lewis, Farhana T. Malik, Benjamin Rumney, Andrew R. Parker, Laura Paletto, and Nick White
- Subjects
0301 basic medicine ,Ostracod ,Cell Survival ,Cell ,Culture ,Cell Culture Techniques ,Crustacean ,Biology ,Article ,03 medical and health sciences ,Animal Shells ,Crustacea ,medicine ,Animals ,Viability assay ,Carapace ,Cell Proliferation ,integumentary system ,04 agricultural and veterinary sciences ,Cell Biology ,General Medicine ,X-Ray Microtomography ,In vitro ,Cell biology ,Disinfection ,030104 developmental biology ,medicine.anatomical_structure ,Epidermal Cells ,Cell culture ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Stem cell ,Epidermal ,Developmental biology ,Microdissection ,Developmental Biology ,Explant culture - Abstract
Primary crustacean cell culture was introduced in the 1960s, but to date limited cell lines have been established. Skogsbergia lerneri is a myodocopid ostracod, which has a body enclosed within a thin, durable, transparent bivalved carapace, through which the eye can see. The epidermal layer lines the inner surface of the carapace and is responsible for carapace synthesis. The purpose of the present study was to develop an in vitro epidermal tissue and cell culture method for S. lerneri. First, an optimal environment for the viability of this epidermal tissue was ascertained, while maintaining its cell proliferative capacity. Next, a microdissection technique to remove the epidermal layer for explant culture was established and finally, a cell dissociation method for epidermal cell culture was determined. Maintenance of sterility, cell viability and proliferation were key throughout these processes. This novel approach for viable S. lerneri epidermal tissue and cell culture augments our understanding of crustacean cell biology and the complex biosynthesis of the ostracod carapace. In addition, these techniques have great potential in the fields of biomaterial manufacture, the military and fisheries, for example, in vitro toxicity testing.
- Published
- 2020
34. Simulation Models Predicting Pressure Distribution and Transmission Underneath Blood Pressure Cuffs of Different Types
- Author
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Prasad Potluri, Philip S. Lewis, Parthasarathi Mandal, and Shenela Naqvi
- Subjects
Blood pressure cuffs ,Polymers and Plastics ,Transmission (telecommunications) ,Distribution (number theory) ,business.industry ,Process Chemistry and Technology ,Simulation modeling ,Materials Chemistry ,Medicine ,Mechanics ,business ,Finite element method - Abstract
Inflatable cuffs of different types are used for the measurement of blood pressure using the indirect method. It is crucial to find pressure distribution and transmission underneath different types of blood pressure measurement cuffs for estimating accurate values of blood pressure. In this study, three simulation models are developed mimicking blood pressure measurement through three cuffs constructed using fabrics that have dissimilar geometric and mechanical properties. Finite element analysis (FEA) is carried out to predict pressure distribution and transmission underneath these cuffs. For validation of these models, an arm simulator was developed. The models provide good agreement with the experimental results. The pressure distribution at the interface of the selected cuffs and arm is not identical.
- Published
- 2020
- Full Text
- View/download PDF
35. A role for NPY-NPY2R signaling in albuminuric kidney disease
- Author
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Robert G. Nelson, Matthias Kretzler, Abigail C Lay, Viji Nair, Christopher R. Neal, Gavin I. Welsh, Jenny A Hurcombe, Marieangela C. Wilson, Raina D. Ramnath, Philip A. Lewis, A Fern Barrington, Kate J. Heesom, Wenjun Ju, Matthew J. Butler, Craig A. McArdle, Mark A. Graham, Denize Atan, Rebecca M. Perrett, Edward Mountjoy, Richard J M Coward, Simon C. Satchell, and Eleanor Herbert
- Subjects
Male ,Proteomics ,medicine.medical_specialty ,Medical Sciences ,Bristol Heart Institute ,Kidney Glomerulus ,Down-Regulation ,urologic and male genital diseases ,Arginine ,Podocyte ,Diabetes Mellitus, Experimental ,Diabetic nephropathy ,Mice ,Diabetes mellitus ,Internal medicine ,mental disorders ,medicine ,Albuminuria ,Animals ,Humans ,Insulin ,Diabetic Nephropathies ,Neuropeptide Y ,PI3K/AKT/mTOR pathway ,Mice, Knockout ,Kidney ,Mice, Inbred BALB C ,Multidisciplinary ,business.industry ,urogenital system ,Podocytes ,NFAT ,Biological Sciences ,Benzazepines ,medicine.disease ,humanities ,Receptors, Neuropeptide Y ,Disease Models, Animal ,medicine.anatomical_structure ,Endocrinology ,Doxorubicin ,Kidney Diseases ,medicine.symptom ,business ,Kidney disease ,Signal Transduction - Abstract
Significance Neuropeptide Y (NPY) is implicated in many pathological conditions including obesity, diabetes, and insulin resistance. However, a pathogenic role of NPY in kidney disease has not been described. We found that NPY is produced by the podocyte in the glomerulus, and this production decreases in renal disease, in contrast to an increase in circulating NPY levels. In the glomerulus, NPY signals via the NPY receptor 2 (NPY2R) and modulates PI3K, MAPK, and NFAT signaling, along with RNA processing and cell migration and, if prolonged, predicted nephrotoxicity. The pharmacological inhibition of NPY-NPY2R signaling also protected against albuminuria and kidney disease in a mouse model of glomerulosclerosis, suggesting that inhibiting this pathway may be therapeutically beneficial in the prevention of kidney disease., Albuminuria is an independent risk factor for the progression to end-stage kidney failure, cardiovascular morbidity, and premature death. As such, discovering signaling pathways that modulate albuminuria is desirable. Here, we studied the transcriptomes of podocytes, key cells in the prevention of albuminuria, under diabetic conditions. We found that Neuropeptide Y (NPY) was significantly down-regulated in insulin-resistant vs. insulin-sensitive mouse podocytes and in human glomeruli of patients with early and late-stage diabetic nephropathy, as well as other nondiabetic glomerular diseases. This contrasts with the increased plasma and urinary levels of NPY that are observed in such conditions. Studying NPY-knockout mice, we found that NPY deficiency in vivo surprisingly reduced the level of albuminuria and podocyte injury in models of both diabetic and nondiabetic kidney disease. In vitro, podocyte NPY signaling occurred via the NPY2 receptor (NPY2R), stimulating PI3K, MAPK, and NFAT activation. Additional unbiased proteomic analysis revealed that glomerular NPY-NPY2R signaling predicted nephrotoxicity, modulated RNA processing, and inhibited cell migration. Furthermore, pharmacologically inhibiting the NPY2R in vivo significantly reduced albuminuria in adriamycin-treated glomerulosclerotic mice. Our findings suggest a pathogenic role of excessive NPY-NPY2R signaling in the glomerulus and that inhibiting NPY-NPY2R signaling in albuminuric kidney disease has therapeutic potential.
- Published
- 2020
- Full Text
- View/download PDF
36. In Vitro Topical Delivery of Chlorhexidine to the Cornea: Enhancement Using Drug-Loaded Contact Lenses and β-Cyclodextrin Complexation, and the Importance of Simulating Tear Irrigation
- Author
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Andrea Brancale, Charles Martin Heard, David Whitaker, Melissa Fallon, Matthew J. Burton, Carmine Varricchio, Hannah M. Boostrom, Philip N. Lewis, Siân R. Morgan, Peter W. J. Morrison, Andrew J. Quantock, and Melissa G. Hewitt
- Subjects
Drug ,medicine.medical_specialty ,Corneal Infection ,Contact Lenses ,Swine ,media_common.quotation_subject ,Pharmaceutical Science ,02 engineering and technology ,030226 pharmacology & pharmacy ,Keratitis ,Cornea ,03 medical and health sciences ,Drug Delivery Systems ,0302 clinical medicine ,Anti-Infective Agents ,Ophthalmology ,Drug Discovery ,medicine ,Animals ,media_common ,chemistry.chemical_classification ,Cyclodextrin ,Chemistry ,Chlorhexidine ,beta-Cyclodextrins ,Hydrogels ,021001 nanoscience & nanotechnology ,medicine.disease ,eye diseases ,In vitro ,Contact lens ,medicine.anatomical_structure ,Tears ,Molecular Medicine ,sense organs ,Ophthalmic Solutions ,0210 nano-technology ,medicine.drug - Abstract
Microbial keratitis is a severe, sight-threatening condition caused by various pathogens. Eyedrops are the standard delivery modality for treating these disorders; however, blinking reflex, elevated tear production, and nasolacrimal drainage eliminate much of the instilled dose within a few seconds. Therefore, eyedrops must be applied repeatedly for prolonged periods. The present study aimed to probe more effective ocular delivery of chlorhexidine based upon drug-loaded hydrogel contact lenses and β-cyclodextrin (β-CD), while also determining the effect of constant irrigation with simulated tear fluid (STF) in in vitro experiments. Chlorhexidine digluconate (as 0.2 and 2% solutions, β-CD inclusion complexes, and loaded hydrogel contact lenses) were applied to enucleated porcine eyes as single or multiple 10 μL doses, or as drug-loaded contact lenses, with and without β-CD. The corneas were then excised and drug-extracted quantified by high-performance liquid chromatography (HPLC). The effect of constant irrigation by STF was evaluated to test the effect of increased tear production on corneal delivery. Potential antimicrobial activity of the delivered drug was also assessed. Results showed that drug-loaded contact lenses delivered the greatest amount of chlorhexidine into the cornea over a 24 h period, while the eyedrop solution comparator delivered the least. The β-CD significantly enhanced chlorhexidine delivery to the cornea from eyedrop solution, although contact lenses loaded with chlorhexidine−β-CD failed to enhance delivery. β-CD within the hydrogel matrix impeded drug release. Constant irrigation with STF significantly reduced the amount of drug delivered to the cornea in all cases. Chlorhexidine retained antimicrobial activity in all delivery methods. Hydrogel contact lenses loaded with chlorhexidine delivered significantly higher levels to the cornea compared to eyedrops, either multiple hourly doses or a single dose. They also offer reduced application, in particular, to a nonulcerated corneal infection. Finally, the importance of fully accounting for tear production in in vitro ocular delivery experiments was highlighted.
- Published
- 2020
- Full Text
- View/download PDF
37. The ultrastructural development and 3D reconstruction of the transparent carapace of the ostracod Skogsbergia lerneri
- Author
-
Benjamin M. Rumney, F. Tegwen Malik, Siân R. Morgan, Andrew R. Parker, Simon Holden, Julie Albon, Philip N. Lewis, and Keith M. Meek
- Subjects
Ecology ,Aquatic Science ,Ecology, Evolution, Behavior and Systematics - Abstract
The Skogsbergia lerneri is a marine ostracod which possesses a carapace that is both protective and transparent. Since development of this carapace and how it is maintained in the adult is not known, the aim of this investigation was to carry out an in-depth ultrastructural study of the ostracod carapace at different developmental stages. Standard transmission electron microscopy and novel serial block face scanning electron microscopy (SBF-SEM) were undertaken to discern carapace ultrastructure in both two and three dimensions. Analysis revealed a carapace consisting of the same basic layer structure as other myodocopid ostracods, namely an epicuticle, exocuticle, endocuticle and membranous layer, but with a thinner adult carapace of mean thickness of 19.2 ± 1.78 µm, n = 5. The carapace layers, except for instar 1 ostracods, had similar relative proportions throughout development. The endocuticle and membranous layer thickened through advancing developmental stages due to an increase in calcified crystalline polyhedrons and a greater number of chitinous lamellae in the membranous layer. Crystalline polyhedron dimensions were significantly smaller near the boundary with the membranous layer. The borders between the carapace layers were indistinct; SBF-SEM revealed an abundance of epicuticle projections into the exocuticle and apparent gradual merging at the boundary of the exocuticle and the endocuticle. Here, we discuss how the S. lerneri carapace layer structure has evolved to serve a specific mechanical function, allowing surface protection and rigidity. In addition, we suggest that the lack of pigment and graduated layer boundaries contribute to the transparency of the carapace.
- Published
- 2022
38. Design and Performance of an Assertional Concurrency Control System.
- Author
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Arthur J. Bernstein, David Scott Gerstl, Wai-Hong Leung, and Philip M. Lewis
- Published
- 1998
- Full Text
- View/download PDF
39. A Theory of Testing for Soft Real-Time Processes.
- Author
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Rance Cleaveland, Insup Lee 0001, Philip M. Lewis, and Scott A. Smolka
- Published
- 1996
40. The Concurrency Factory: A Development Environment for Concurrent Systems.
- Author
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Rance Cleaveland, Philip M. Lewis, Scott A. Smolka, and Oleg Sokolsky
- Published
- 1996
- Full Text
- View/download PDF
41. The Concurrency Factory Software Development Environment.
- Author
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Rance Cleaveland, Philip M. Lewis, Scott A. Smolka, and Oleg Sokolsky
- Published
- 1996
- Full Text
- View/download PDF
42. An Integrated Approach to Communication Axioms Among Concurrent Processes.
- Author
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Rui Hu and Philip M. Lewis
- Published
- 1995
43. The Concurrency Factory - Practical Tools for Specification, Stimulation, Verification, and Implementation of Concurrent Systems.
- Author
-
Rance Cleaveland, Jayesh N. Gada, Philip M. Lewis, Scott A. Smolka, Oleg Sokolsky, and Shipei Zhang
- Published
- 1994
- Full Text
- View/download PDF
44. Effects of brain tissue oxygen (PbtO
- Author
-
Leanne M C, Hays, Andrew, Udy, Alexios A, Adamides, James R, Anstey, Michael, Bailey, Judith, Bellapart, Kathleen, Byrne, Andrew, Cheng, D, Jamie Cooper, Katharine J, Drummond, Matthias, Haenggi, Stephan M, Jakob, Alisa M, Higgins, Philip M, Lewis, Martin K, Hunn, Robert, McNamara, David K, Menon, Lynne, Murray, Benjamin, Reddi, Tony, Trapani, Shirley, Vallance, Paul J, Young, Ramon, Diaz-Arrastia, Lori, Shutter, Patrick T, Murray, Gerard F, Curley, and Alistair, Nichol
- Subjects
Oxygen ,Intracranial Pressure ,Brain Injuries, Traumatic ,Brain ,Glasgow Outcome Scale ,Humans - Abstract
Monitoring and optimisation of brain tissue oxygen tension (PbtO
- Published
- 2021
45. The United States, globalisation, and health and safety
- Author
-
Philip G. Lewis and Edward A. Emmett
- Subjects
Globalization ,Economic growth ,Political science ,Occupational safety and health - Published
- 2021
- Full Text
- View/download PDF
46. Characterisation of carapace composition in developing and adult ostracods (
- Author
-
Benjamin M, Rumney, Siân R, Morgan, J Frederick W, Mosselmans, F Tegwen, Malik, Simon J, Holden, Andrew R, Parker, Nick, White, Philip N, Lewis, Julie, Albon, and Keith M, Meek
- Abstract
The protective carapace of
- Published
- 2021
47. Algorithms, Algebra, and the Computer Lab.
- Author
-
Philip G. Lewis
- Published
- 1992
- Full Text
- View/download PDF
48. The ultrastructural development and 3D reconstruction of the transparent carapace of the ostracod
- Author
-
Benjamin M, Rumney, F Tegwen, Malik, Siân R, Morgan, Andrew R, Parker, Simon, Holden, Julie, Albon, Philip N, Lewis, and Keith M, Meek
- Abstract
TheThe online version contains supplementary material available at 10.1007/s00227-021-04006-7.
- Published
- 2021
49. Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching
- Author
-
Mary J. O'Connell, Julie L Aspden, Juan Fontana, Karl Norris, Philip A. Lewis, Michaela Agapiou, Charley G. P. McCarthy, and Tayah Hopes
- Subjects
Male ,Ribosomal Proteins ,animal structures ,Ovary (botany) ,Ovary ,Biology ,Ribosome ,03 medical and health sciences ,0302 clinical medicine ,Ribosomal protein ,Testis ,Genetics ,medicine ,Animals ,030304 developmental biology ,0303 health sciences ,fungi ,Translation (biology) ,Ribosomal RNA ,biology.organism_classification ,Cell biology ,medicine.anatomical_structure ,Drosophila melanogaster ,Homogeneous ,Protein Biosynthesis ,Female ,Eukaryotic Ribosome ,Ribosomes ,030217 neurology & neurosurgery - Abstract
Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 4 tissues of Drosophila melanogaster. We find that testes and ovaries contain the most heterogeneous ribosome populations, which occurs through a combination of paralog-enrichment and paralog-switching. We have solved structures of ribosomes purified from in vivo tissues by cryo-EM, revealing differences in precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-switching could alter the ribosome surface, enabling different proteins to regulate translation. One testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of ribosome heterogeneity. Overall, this work allows us to propose that mRNA translation might be regulated in the gonads through ribosome heterogeneity, providing a potential means of ribosome specialisation.
- Published
- 2021
50. Sorting nexin-27 regulates AMPA receptor trafficking through the synaptic adhesion protein LRFN2
- Author
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Paul J Banks, Zafar I. Bashir, Philip A. Lewis, Brett M. Collins, Kirsty J McMillan, Peter J. Cullen, Ruth E. Carmichael, Jeremy M. Henley, Kevin A. Wilkinson, Thomas Clairfeuille, Kate J. Heesom, Francesca L N Hellel, and Ashley J. Evans
- Subjects
0301 basic medicine ,Proteomics ,SNX27 ,Long-Term Potentiation ,Excitotoxicity ,medicine.disease_cause ,Hippocampus ,Synaptic Transmission ,0302 clinical medicine ,Biology (General) ,AMPA receptors ,Integral membrane protein ,Sorting Nexins ,Neurons ,0303 health sciences ,Membrane Glycoproteins ,Chemistry ,General Neuroscience ,membrane trafficking ,Long-term potentiation ,General Medicine ,Cell biology ,Protein Transport ,Medicine ,Research Article ,Human ,QH301-705.5 ,Endosome ,Science ,Nerve Tissue Proteins ,AMPA receptor ,Endosomes ,Neurotransmission ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,medicine ,Animals ,Humans ,Receptors, AMPA ,030304 developmental biology ,Memory Disorders ,General Immunology and Microbiology ,Cell Biology ,Rats ,Sorting nexin ,030104 developmental biology ,LRFN2 ,Rat ,030217 neurology & neurosurgery ,Neuroscience - Abstract
The endosome-associated cargo adaptor sorting nexin-27 (SNX27) is linked to various neuropathologies through sorting of integral proteins to the synaptic surface, most notably AMPA receptors. To provide a broader view of SNX27-associated pathologies we have performed unbiased proteomics to identify new neuronal SNX27-dependent cargoes, and identified proteins linked to excitotoxicity (SLC1A3, SLC4A7, SLC6A11), epilepsy, intellectual disabilities and working memory deficits (KCNT2, ADAM22, KIDINS220, LRFN2). Focusing on the synaptic adhesion molecule leucine-rich repeat and fibronectin type-III domain-containing protein 2 (LRFN2), we establish that SNX27 binds to LRFN2 and is responsible for regulating its endosomal sorting. LRFN2 associates with AMPA receptors and knockdown of LRFN2 phenocopies SNX27 depletion in decreasing surface expression of AMPA receptors, reducing synaptic activity and attenuating hippocampal long-term potentiation. Our evidence suggests that, in contrast to previous reports, SNX27 does not directly bind to AMPA receptors, and instead controls AMPA receptor-mediated synaptic transmission and plasticity indirectly through the endosomal sorting of LRFN2. Overall, our study provides new molecular insight into the perturbed function of SNX27 and LRFN2 in a range of neurological conditions.
- Published
- 2021
- Full Text
- View/download PDF
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