Publications by authors named "Sam Janes"

Introduction: Low dose CT (LDCT) screening for lung cancer reduces lung cancer mortality, but there is a lack of international consensus regarding the optimal eligibility criteria for screening. The Yorkshire Lung Screening Trial (YLST) was designed to evaluate lung cancer screening (LCS) implementation and a primary objective was prospective evaluation of 3 pre-defined eligibility criteria.

Methods: Individuals who had ever smoked, aged 55-80yrs, who responded to written invitation, underwent telephone risk assessment and if eligible by at least one criteria (PLCO≥1.

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Article Synopsis
  • Synthetic data offers a way to share healthcare information without compromising privacy, showing promise for research and development.
  • Unlike other methods like federated learning, synthetic data allows analyses to be conducted without needing to adjust the data format, making it versatile for various applications.
  • The study developed synthetic data for ever-smokers in the UK Biobank to create lung cancer prognostic models, demonstrating its effectiveness throughout the modeling process and exploring the impacts of different data sharing methods in healthcare.
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  • Lung cancer screening (LCS) programs are becoming more common globally, but they differ in how they're run, who qualifies, and how resources are used.
  • Very few LCS programs are fully established on a national level, though more are expected to be developed soon.
  • Combining low-dose chest CT scans with smoking cessation support has shown to improve patient outcomes, and promising technologies like risk prediction models and AI are being explored, but they still need more research and validation before being widely implemented.
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Basal cells are adult stem cells in the airway epithelium and regenerate differentiated cell populations, including the mucosecretory and ciliated cells that enact mucociliary clearance. Human basal cells can proliferate and produce differentiated epithelium in vitro. However, studies of airway epithelial differentiation mostly rely on immunohistochemical or immunofluorescence-based staining approaches, meaning that a dynamic approach is lacking, and quantitative data are limited.

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Article Synopsis
  • - This study addresses the challenges of accurately segmenting airway trees in the context of diagnosing and characterizing chronic respiratory diseases, emphasizing the limitations of existing traditional methods requiring manual adjustments due to inconsistent segmentation results.
  • - It introduces a novel deep learning approach called Interpolation-Split, which enhances segmentation performance by improving data quality through interpolation and image splitting, while also being efficient in terms of computational resource usage.
  • - The results show that this new method significantly outperforms previous models in segmentation accuracy, achieving high dice similarity coefficients while requiring less GPU memory, making it more accessible for various computational environments.
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Background: Human bone marrow mesenchymal stem cell (MSC) administration reduces inflammation in pre-clinical models of sepsis and sepsis-related lung injury, however clinical efficacy in patients has not yet been demonstrated. We previously showed that Alveolar Macrophage (AM) 11β-hydroxysteroid dehydrogenase type-1 (HSD-1) autocrine signalling is impaired in critically ill sepsis patients, which promotes inflammatory injury. Administration of transgenic MSCs (tMSCs) which overexpress HSD-1 may enhance the anti-inflammatory effects of local glucocorticoids and be more effective at reducing inflammation in sepsis than cellular therapy alone.

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  • The study investigates early cellular responses to SARS-CoV-2 infection using single-cell profiling in individuals with no prior immunity to the virus.
  • Significant changes in cell types and immune responses were observed over time, indicating different patterns of infection severity, especially in nasopharyngeal regions.
  • Key findings suggest that early interferon responses and specific immune cell behaviors, like high expression of HLA-DQA2, could be crucial in preventing sustained infections, while a novel computational tool, Cell2TCR, enhanced the analysis of T cell responses.
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Lung cancer screening (LCS) using annual computed tomography (CT) scanning significantly reduces mortality by detecting cancerous lung nodules at an earlier stage. Deep learning algorithms can improve nodule malignancy risk stratification. However, they have typically been used to analyse single time point CT data when detecting malignant nodules on either baseline or incident CT LCS rounds.

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Patient-derived xenograft (PDX) models are widely used in cancer research. To investigate the genomic fidelity of non-small cell lung cancer PDX models, we established 48 PDX models from 22 patients enrolled in the TRACERx study. Multi-region tumor sampling increased successful PDX engraftment and most models were histologically similar to their parent tumor.

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Acute injury in the airways or the lung activates local progenitors and stimulates changes in cell-cell interactions to restore homeostasis, but it is not appreciated how more distant niches are impacted. We utilized mouse models of airway-specific epithelial injury to examine secondary tissue-wide alveolar, immune, and mesenchymal responses. Single-cell transcriptomics and validation revealed transient, tissue-wide proliferation of alveolar type 2 (AT2) progenitor cells after club cell-specific ablation.

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The hallmark of epidermolysis bullosa (EB) is fragile attachment of epithelia due to genetic variants in cell adhesion genes. We describe 16 EB patients treated in the ear, nose, and throat department of a tertiary pediatric hospital linked to the United Kingdom's national EB unit between 1992 and 2023. Patients suffered a high degree of morbidity and mortality from laryngotracheal stenosis.

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The upper airway acts as a conduit for the passage of air to the respiratory system and is implicated in several chronic diseases. Whilst the cell biology of the distal respiratory system has been described in great detail, less is known about the proximal upper airway. In this review, we describe the relevant anatomy of the upper airway and discuss the literature detailing the identification and roles of the progenitor cells of these regions.

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Machine learning (ML)-based risk prediction models hold the potential to support the health-care setting in several ways; however, use of such models is scarce. We aimed to review health-care professional (HCP) and patient perceptions of ML risk prediction models in published literature, to inform future risk prediction model development. Following database and citation searches, we identified 41 articles suitable for inclusion.

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Background: Lung cancer clinical guidelines and risk tools often rely on smoking history as a significant risk factor. However, never-smokers make up 14% of the lung cancer population, and this proportion is rising. Consequently, they are often perceived as low-risk and may experience diagnostic delays.

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Introduction: Early cancer detection can significantly improve patient outcomes and reduce mortality rates. Novel cancer screening approaches, including multi-cancer early detection tests, have been developed. Cost-utility analyses will be needed to examine their value, and these models require health state utilities.

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Introduction: In a small percentage of patients, pulmonary nodules found on CT scans are early lung cancers. Lung cancer detected at an early stage has a much better prognosis. The British Thoracic Society guideline on managing pulmonary nodules recommends using multivariable malignancy risk prediction models to assist in management.

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Studies of human lung development have focused on epithelial and mesenchymal cell types and function, but much less is known about the developing lung immune cells, even though the airways are a major site of mucosal immunity after birth. An unanswered question is whether tissue-resident immune cells play a role in shaping the tissue as it develops in utero. Here, we profiled human embryonic and fetal lung immune cells using scRNA-seq, smFISH, and immunohistochemistry.

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Article Synopsis
  • A study on combined pulmonary fibrosis and emphysema (CPFE) explored how these conditions impact mortality and lung function decline compared to patients with just idiopathic pulmonary fibrosis (IPF).
  • CPFE patients with more than 10% emphysema had a history of stronger smoking habits and experienced more pronounced declines in lung function, particularly in diffusing capacity, which correlated better with mortality than overall lung capacity measures.
  • The findings suggest that when evaluating disease progression in IPF, specific measures like diffusing capacity should be prioritized for patients with significant emphysema, while a relative decline in forced vital capacity (FVC) should be monitored in non-CPFE IPF patients.
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Background: Risk-based screening for lung cancer is currently being considered in several countries; however, the optimal approach to determine eligibility remains unclear. Ensemble machine learning could support the development of highly parsimonious prediction models that maintain the performance of more complex models while maximising simplicity and generalisability, supporting the widespread adoption of personalised screening. In this work, we aimed to develop and validate ensemble machine learning models to determine eligibility for risk-based lung cancer screening.

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Introduction: COPD is underdiagnosed, and measurement of spirometry alongside low-dose computed tomography (LDCT) screening for lung cancer is one strategy to increase earlier diagnosis of this disease.

Methods: Ever-smokers at high risk of lung cancer were invited to the Yorkshire Lung Screening Trial for a lung health check (LHC) comprising LDCT screening, pre-bronchodilator spirometry and a smoking cessation service. In this cross-sectional study we present data on participant demographics, respiratory symptoms, lung function, emphysema on imaging and both self-reported and primary care diagnoses of COPD.

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Lung infections are one of the leading causes of death worldwide, and this situation has been exacerbated by the emergence of COVID-19. Pre-clinical modelling of viral infections has relied on cell cultures that lack 3D structure and the context of lung extracellular matrices. Here, we propose a bioreactor-based, whole-organ lung model of viral infection.

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Objectives: The study examined whether quantified airway metrics associate with mortality in idiopathic pulmonary fibrosis (IPF).

Methods: In an observational cohort study (n = 90) of IPF patients from Ege University Hospital, an airway analysis tool AirQuant calculated median airway intersegmental tapering and segmental tortuosity across the 2nd to 6th airway generations. Intersegmental tapering measures the difference in median diameter between adjacent airway segments.

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