Transcriptomic Plasticity of Human Alveolar Macrophages Revealed by Single-Cell RNA Sequencing Following Drug Exposure: Implications for Therapeutic Development.

Alveolar macrophages (AM) must perform three seemingly opposing roles including homeostasis, driving inflammation, and facilitating tissue repair. Whilst there is now consensus (supported by a large body of human single cell RNA sequencing (scRNA-seq) data) that the cell subsets that perform these tasks can readily be found based on their transcriptome, their ontogeny has remained unclear. Moreover, there is agreement that in all types of pulmonary fibrosis (PF) there is an expanded population of profibrotic AM that may aberrantly drive PF.

Prioritizing educational technologies for children with intellectual disabilities under fuzzy MCDM perspective.

Children with intellectual disabilities struggled to perform basic tasks in the educational platform due to their deferred learning pace and individual challenges. To assist such needs, the child's individual education program (IEP) team, spearheaded by the school administrators, continues to offer supplementary educational technologies. However, selecting an appropriate technology does not follow an objective system, making the decision process tedious and unreliable.

Estimating the force of infection of four dengue serotypes from serological studies in two regions of Vietnam.

Dengue is endemic in Vietnam with circulation of all four serotypes (DENV1-4) all year-round. It is hard to estimate the disease's true serotype-specific transmission patterns from cases due to its high asymptomatic rate, low reporting rate and complex immunity and transmission dynamics. Seroprevalence studies have been used to great effect for understanding patterns of dengue transmission.

Differences in virus and immune dynamics for SARS-CoV-2 Delta and Omicron infections by age and vaccination histories.

Vaccination against COVID-19 was integral to controlling the pandemic that persisted with the continuous emergence of SARS-CoV-2 variants. Using a mathematical model describing SARS-CoV-2 within-host infection dynamics, we estimate differences in virus and immunity due to factors of infecting variant, age, and vaccination history (vaccination brand, number of doses and time since vaccination). We fit our model in a Bayesian framework to upper respiratory tract viral load measurements obtained from cases of Delta and Omicron infections in Singapore, of whom the majority only had one nasopharyngeal swab measurement.

Immunological Landscapes in Lung Transplantation: Insights from T Cell Profiling in BAL and PBMC.

Lung transplant recipients frequently encounter immune-related complications, including chronic lung allograft dysfunction (CLAD). Monitoring immune cells within the lung microenvironment is pivotal for optimizing post-transplant outcomes. This study examined the proportion of T cell subsets in paired bronchoalveolar lavage (BAL) and peripheral PBMC comparing healthy ( = 4) and lung transplantation patients ( = 6, no CLAD and = 14 CLAD) using 14-color flow cytometry.

Causal relationships between breast cancer risk factors based on mammographic features.

Background: Mammogram risk scores based on texture and density defined by different brightness thresholds are associated with breast cancer risk differently and could reveal distinct information about breast cancer risk. We aimed to investigate causal relationships between these intercorrelated mammogram risk scores to determine their relevance to breast cancer aetiology.

Methods: We used digitised mammograms for 371 monozygotic twin pairs, aged 40-70 years without a prior diagnosis of breast cancer at the time of mammography, from the Australian Mammographic Density Twins and Sisters Study.

Uncovering the magnitude of African pangolin poaching with extensive nanopore DNA genotyping of seized scales.

Trade in pangolins is illegal, and yet tons of their scales and products are seized at various ports. These large seizures are challenging to process and comprehensively genotype for upstream provenance tracing and species identification for prosecution. We implemented a scalable DNA barcoding pipeline in which rapid DNA extraction and MinION sequencing were used to genotype a substantial proportion of pangolin scales subsampled from 2 record shipments seized in Singapore in 2019 (37.

Gradual Self-Training via Confidence and Volume Based Domain Adaptation for Multi Dataset Deep Learning-Based Brain Metastases Detection Using Nonlocal Networks on MRI Images.

Background: Research suggests that treatment of multiple brain metastases (BMs) with stereotactic radiosurgery shows improvement when metastases are detected early, providing a case for BM detection capabilities on small lesions.

Purpose: To demonstrate automatic detection of BM on three MRI datasets using a deep learning-based approach. To improve the performance of the network is iteratively co-trained with datasets from different domains.

Genetic Aspects of Mammographic Density Measures Associated with Breast Cancer Risk.

Cumulus, Altocumulus, and Cirrocumulus are measures of mammographic density defined at increasing pixel brightness thresholds, which, when converted to mammogram risk scores (MRSs), predict breast cancer risk. Twin and family studies suggest substantial variance in the MRSs could be explained by genetic factors. For 2559 women aged 30 to 80 years (mean 54 years), we measured the MRSs from digitized film mammograms and estimated the associations of the MRSs with a 313-SNP breast cancer polygenic risk score (PRS) and 202 individual SNPs associated with breast cancer risk.

Familial Aspects of Mammographic Density Measures Associated with Breast Cancer Risk.

, , , and are mammogram risk scores (MRSs) for breast cancer based on mammographic density defined in effect by different levels of pixel brightness and adjusted for age and body mass index. We measured these MRS from digitized film mammograms for 593 monozygotic (MZ) and 326 dizygotic (DZ) female twin pairs and 1592 of their sisters. We estimated the correlations in relatives () and the proportion of variance due to genetic factors (heritability) using the software FISHER and predicted the familial risk ratio (FRR) associated with each MRS.

Alveolar crystal burden in stone workers with artificial stone silicosis.

Background And Objective: An epidemic of silicosis has emerged due to a failure to control risks associated with exposure to high-silica content respirable dust generated while working with artificial stone products. Methods for quantification of alveolar crystal burden are needed to advance our understanding of the pathobiology of silica-related lung injury as well as assisting in the diagnosis, clinical management and prognostication of affected workers. The objective of this study was to develop and validate novel methods to quantify alveolar crystal burden in bronchoalveolar lavage (BAL) fluid from patients with artificial stone silicosis.

TELO-SCOPE study: a randomised, double-blind, placebo-controlled, phase 2 trial of danazol for short telomere related pulmonary fibrosis.

Introduction: Recent discoveries have identified shortened telomeres and related mutations in people with pulmonary fibrosis (PF). There is evidence to suggest that androgens, including danazol, may be effective in lengthening telomeres in peripheral blood cells. This study aims to assess the safety and efficacy of danazol in adults and children with PF associated with telomere shortening.

Inferior outcomes in lung transplant recipients with serum Pseudomonas aeruginosa specific cloaking antibodies.

Background: Chronic Lung Allograft Dysfunction (CLAD) limits long-term survival following lung transplantation. Colonization of the allograft by Pseudomonas aeruginosa is associated with an increased risk of CLAD and inferior overall survival. Recent experimental data suggests that 'cloaking' antibodies targeting the O-antigen of the P.

3D axial-attention for lung nodule classification.

Purpose: In recent years, Non-Local-based methods have been successfully applied to lung nodule classification. However, these methods offer 2D attention or limited 3D attention to low-resolution feature maps. Moreover, they still depend on a convenient local filter such as convolution as full 3D attention is expensive to compute and requires a big dataset, which might not be available.

Airway Telomere Length in Lung Transplant Recipients.

Introduction: Chronic lung allograft dysfunction (CLAD) represents the major impediment to long term survival following lung transplantation. Donor and recipient telomere length have been shown to associate with lung transplant outcomes, including CLAD. In this study we aimed to measure the telomere lengths of bronchial and bronchiolar airway cells in lung allografts early after transplantation and to investigate associations with CLAD and all-cause mortality.

The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom.

Diatoms are major contributors to global primary production and their populations in the modern oceans are affected by availability of iron, nitrogen, phosphate, silica, and other trace metals, vitamins, and infochemicals. However, little is known about the role of phosphorylation in diatoms and its role in regulation and signaling. We report a total of 2759 phosphorylation sites on 1502 proteins detected in .

Pulmonary alveolar proteinosis after lung transplantation.

We report the case of a 69-year-old man five-month post double lung transplant for idiopathic pulmonary fibrosis (IPF) who presented with progressive breathlessness, loss of lung function, and diffuse ground glass shadowing on the chest computed tomography. Transbronchial lung biopsy revealed foamy macrophages, hyperplasia of type II pneumocytes, and eosinophilic material in the alveolar space. Video thoracic lung biopsy was performed, and histology confirmed pulmonary alveolar proteinosis.

Multiplexed Knockouts in the Model Diatom by Episomal Delivery of a Selectable Cas9.

Marine diatoms are eukaryotic microalgae that play significant ecological and biogeochemical roles in oceans. They also have significant potential as organismal platforms for exploitation to address biotechnological and industrial goals. In order to address both modes of research, sophisticated molecular and genetic tools are required.

Measurement challenge: protocol for international case-control comparison of mammographic measures that predict breast cancer risk.

Introduction: For women of the same age and body mass index, increased mammographic density is one of the strongest predictors of breast cancer risk. There are multiple methods of measuring mammographic density and other features in a mammogram that could potentially be used in a screening setting to identify and target women at high risk of developing breast cancer. However, it is unclear which measurement method provides the strongest predictor of breast cancer risk.

Endothelial Glycocalyx Shedding Occurs during Ex Vivo Lung Perfusion: A Pilot Study.

Background: Damage to the endothelium has been established as a key pathological process in lung transplantation and ex vivo lung perfusion (EVLP), a new technology that provides a platform for the assessment of injured donor lungs. Damage to the lung endothelial glycocalyx, a structure that lines the endothelium and is integral to vascular barrier function, has been associated with lung dysfunction. We hypothesised that endothelial glycocalyx shedding occurs during EVLP and aimed to establish a porcine model to investigate the mechanism underlying glycocalyx breakdown during EVLP.

Lung nodule classification using deep Local-Global networks.

Purpose: Lung nodules have very diverse shapes and sizes, which makes classifying them as benign/malignant a challenging problem. In this paper, we propose a novel method to predict the malignancy of nodules that have the capability to analyze the shape and size of a nodule using a global feature extractor, as well as the density and structure of the nodule using a local feature extractor.

Methods: We propose to use Residual Blocks with a 3 × 3 kernel size for local feature extraction and Non-Local Blocks to extract the global features.