Pulmonary Challenge Research Articles

Metric learning guided sinogram denoising for cone beam CT enhancement.

Cone beam computed tomography (CBCT) is a widely available modality, but its clinical utility has been limited by low detail conspicuity and quantitative accuracy. Convenient post-reconstruction denoising is subject to back projected patterned residual, but joint denoise-reconstruction is typically computationally expensive and complex. In this study, we develop and evaluate a novel Metric-learning guided wavelet transform reconstruction (MEGATRON) approach to enhance image domain quality with projection-domain processing. Projection domain based processing has the benefit of being simple, efficient, and compatible with various reconstruction toolkit and vendor platforms. However, they also typically show inferior performance in the final reconstructed image, because the denoising goals in projection and image domains do not necessarily align. Motivated by these observations, this work aims to translate the demand for quality enhancement from the quantitative image domain to the more easily operable projection domain. Specifically, the proposed paradigm consists of a metric learning module and a denoising network module. Via metric learning, enhancement objectives on the wavelet encoded sinogram domain data are defined to reflect post-reconstruction image discrepancy. The denoising network maps measured cone-beam projection to its enhanced version, driven by the learnt objective. In doing so, the denoiser operates in the convenient sinogram to sinogram fashion but reflects improvement in reconstructed image as the final goal. Implementation-wise, metric learning was formalized as optimizing the weighted fitting of wavelet subbands, and a res-Unet, which is a Unet structure with residual blocks, was used for denoising. To access quantitative reference, cone-beam projections were simulated using the X-ray based Cancer Imaging Simulation Toolkit (XCIST). In both learning modules, a data set of 123 human thoraxes, which was from Open-Source Imaging Consortium (OSIC) Pulmonary Fibrosis Progression challenge, was used. Reconstructed CBCT thoracic images were compared against ground truth FB and performance was assessed in root mean square error (RMSE), peak signal-to-noise ratio (PSNR), and structural similarity index (SSIM). MEGATRON achieved RMSE in HU value, PSNR, and SSIM were 30.97±4.25, 37.45±1.78, and 93.23±1.62, respectively. These values are on par with reported results from sophisticated physics-driven CBCT enhancement, demonstrating promise and utility of the proposed MEGATRON method. We have demonstrated that incorporating the proposed metric learning into sinogram denoising introduces awareness of reconstruction goal and improves final quantitative performance. The proposed approach is compatible with a wide range of denoiser network structures and reconstruction modules, to suit customized need or further improve performance.

Blocking HXA3-mediated neutrophil elastase release during S. pneumoniae lung infection limits pulmonary epithelial barrier disruption and bacteremia.

Streptococcus pneumoniae (Sp), a leading cause of community-acquired pneumonia, can spread from the lung into the bloodstream to cause septicemia and meningitis, with a concomitant threefold increase in mortality. Limitations in vaccine efficacy and a rise in antimicrobial resistance have spurred searches for host-directed therapies that target pathogenic immune processes. Polymorphonuclear leukocytes (PMNs) are essential for infection control but can also promote tissue damage and pathogen spread. The major Sp virulence factor, pneumolysin, triggers acute inflammation by stimulating the 12-lipoxygenase (12-LOX) eicosanoid synthesis pathway in epithelial cells. This pathway is required for systemic spread in a mouse pneumonia model and produces a number of bioactive lipids, including hepoxilin A3 (HXA3), a hydroxy epoxide PMN chemoattractant that has been hypothesized to facilitate breach of mucosal barriers. To understand how 12-LOX-dependent inflammation promotes dissemination during Sp lung infection and dissemination, we utilized bronchial stem cell-derived air-liquid interface cultures that lack this enzyme to show that HXA3 methyl ester (HXA3-ME) is sufficient to promote basolateral-to-apical PMN transmigration, monolayer disruption, and concomitant Sp barrier breach. In contrast, PMN transmigration in response to the non-eicosanoid chemoattractant N-formyl-L-methionyl-L-leucyl-phenylalanine (fMLP) did not lead to epithelial disruption or bacterial translocation. Correspondingly, HXA3-ME but not fMLP increased the release of neutrophil elastase (NE) from Sp-infected PMNs. Pharmacologic blockade of NE secretion or activity diminished epithelial barrier disruption and bacteremia after pulmonary challenge of mice. Thus, HXA3 promotes barrier-disrupting PMN transmigration and NE release, pathological events that can be targeted to curtail systemic disease following pneumococcal pneumonia.IMPORTANCEStreptococcus pneumoniae (Sp), a leading cause of pneumonia, can spread from the lung into the bloodstream to cause systemic disease. Limitations in vaccine efficacy and a rise in antimicrobial resistance have spurred searches for host-directed therapies that limit pathologic host immune responses to Sp. Excessive polymorphonuclear leukocyte (PMN) infiltration into Sp-infected airways promotes systemic disease. Using stem cell-derived respiratory cultures that reflect bona fide lung epithelium, we identified eicosanoid hepoxilin A3 as a critical pulmonary PMN chemoattractant that is sufficient to drive PMN-mediated epithelial damage by inducing the release of neutrophil elastase. Inhibition of the release or activity of this protease in mice limited epithelial barrier disruption and bacterial dissemination, suggesting a new host-directed treatment for Sp lung infection.

ILC2-derived LIF licences progress from tissue to systemic immunity

Migration and homing of immune cells are critical for immune surveillance. Trafficking is mediated by combinations of adhesion and chemokine receptors that guide immune cells, in response to chemokine signals, to specific locations within tissues and the lymphatic system to support tissue-localized immune reactions and systemic immunity1,2. Here we show that disruption of leukaemia inhibitory factor (LIF) production from group 2 innate lymphoid cells (ILC2s) prevents immune cells leaving the lungs to migrate to the lymph nodes (LNs). In the absence of LIF, viral infection leads to plasmacytoid dendritic cells (pDCs) becoming retained in the lungs where they improve tissue-localized, antiviral immunity, whereas chronic pulmonary allergen challenge leads to marked immune cell accumulation and the formation of tertiary lymphoid structures in the lung. In both cases immune cells fail to migrate to the lymphatics, leading to highly compromised LN reactions. Mechanistically, ILC2-derived LIF induces the production of the chemokine CCL21 from lymphatic endothelial cells lining the pulmonary lymphatic vessels, thus licensing the homing of CCR7+ immune cells (including dendritic cells) to LNs. Consequently, ILC2-derived LIF dictates the egress of immune cells from the lungs to regulate tissue-localized versus systemic immunity and the balance between allergen and viral responsiveness in the lungs.

SECRET: Statistical Emulation for Computational Reverse Engineering and Translation with applications in healthcare

There have been impressive advances in the physical and mathematical modelling of complex physiological systems in the last few decades, with the potential to revolutionise personalised healthcare with patient-specific evidence-based diagnosis, risk assessment and treatment decision support using digital twins. However, practical progress and genuine clinical impact hinge on successful model calibration, parameter estimation and uncertainty quantification, which calls for novel innovative adaptions and methodological extensions of contemporary state-of-the-art inference techniques from Statistics and Machine Learning. In the present study, we focus on two computational fluid-dynamics (CFD) models of the blood systemic and pulmonary circulation. We discuss state-of-the-art emulation techniques based on deep learning and Gaussian processes, which are coupled with established inference techniques based on greedy optimisation, simulated annealing, Markov Chain Monte Carlo, History Matching and rejection sampling for computationally fast inference of unknown parameters of the CFD models from blood flow and pressure data. The inference task was set as a competitive challenge which the participants had to conduct within a limited time frame representative of clinical requirements. The performance of the methods was assessed independently and objectively by the challenge organisers, based on a ground truth that was unknown to the method developers. Our results indicate that for the systemic challenge, in which an idealised case of noise-free data was considered, the relative deviation from the ground-truth in parameter space ranges from 10−5% (highest-performing method) to 3% (lowest-performing method). For the pulmonary challenge, for which noisy data was generated, the performance ranges from 0.9% to 7% deviation for the parameter posterior mean, and from 35% to 570% deviation for the parameter posterior variance.

Protection against experimental cryptococcosis elicited by Cationic Adjuvant Formulation 01-adjuvanted subunit vaccines.

The fungal infection, cryptococcosis, is responsible for >100,000 deaths annually. No licensed vaccines are available. We explored the efficacy and immune responses of subunit cryptococcal vaccines adjuvanted with Cationic Adjuvant Formulation 01 (CAF01). CAF01 promotes humoral and T helper (Th) 1 and Th17 immune responses and has been safely used in human vaccine trials. Four subcutaneous vaccines, each containing single recombinant Cryptococcus neoformans protein antigens, partially protected mice from experimental cryptococcosis. Protection increased, up to 100%, in mice that received bivalent and quadrivalent vaccine formulations. Vaccinated mice that received a pulmonary challenge with C. neoformans had an influx of leukocytes into the lung including robust numbers of polyfunctional CD4+ T cells which produced interferon gamma (IFNγ), tumor necrosis factor alpha (TNFα), and interleukin (IL)-17 upon ex vivo antigenic stimulation. Cytokine-producing lung CD8+ T cells were also found, albeit in lesser numbers. A significant, durable IFNγ response was observed in the lungs, spleen, and blood. Moreover, IFNγ secretion following ex vivo stimulation directly correlated with fungal control in the lungs. Thus, we have developed multivalent cryptococcal vaccines which protect mice from experimental cryptococcosis using an adjuvant which has been safely tested in humans. These preclinical studies suggest a path towards human cryptococcal vaccine trials.

Blocking HXA3-mediated neutrophil elastase release during S. pneumoniae lung infection limits pulmonary epithelial barrier disruption and bacteremia.

Streptococcus pneumoniae (Sp), a leading cause of community-acquired pneumonia, can spread from the lung into the bloodstream to cause septicemia and meningitis, with a concomitant three-fold increase in mortality. Limitations in vaccine efficacy and a rise in antimicrobial resistance have spurred searches for host-directed therapies that target pathogenic immune processes. Polymorphonuclear leukocytes (PMNs) are essential for infection control but can also promote tissue damage and pathogen spread. The major Sp virulence factor, pneumolysin (PLY), triggers acute inflammation by stimulating the 12-lipoxygenase (12-LOX) eicosanoid synthesis pathway in epithelial cells. This pathway is required for systemic spread in a mouse pneumonia model and produces a number of bioactive lipids, including hepoxilin A3 (HXA3), a hydroxy epoxide PMN chemoattractant that has been hypothesized to facilitate breach of mucosal barriers. To understand how 12-LOX-dependent inflammation promotes dissemination during Sp lung infection and dissemination, we utilized bronchial stem cell-derived air-liquid interface (ALI) cultures that lack this enzyme to show that HXA3 methyl ester (HXA3-ME) is sufficient to promote basolateral-to-apical PMN transmigration, monolayer disruption, and concomitant Sp barrier breach. In contrast, PMN transmigration in response to the non-eicosanoid chemoattractant fMLP did not lead to epithelial disruption or bacterial translocation. Correspondingly, HXA3-ME but not fMLP increased release of neutrophil elastase (NE) from Sp-infected PMNs. Pharmacologic blockade of NE secretion or activity diminished epithelial barrier disruption and bacteremia after pulmonary challenge of mice. Thus, HXA3 promotes barrier disrupting PMN transmigration and NE release, pathological events that can be targeted to curtail systemic disease following pneumococcal pneumonia.

Intravenous Immunization with Triple Auxotrophs of Mycobacterium tuberculosis : A novel vaccine strategy against tuberculosis.

Tuberculosis, caused by Mycobacterium tuberculosis ( Mtb ), remains a leading infectious cause of mortality worldwide despite widespread use of the BCG vaccine and the availability of sterilizing pharmacopoeia. Recent research indicates that the intravenous administration of BCG confers sterilizing immunity against Mtb pulmonary challenge in non-human primates. However, while BCG is relatively safe, complications such as disseminated BCGosis have been observed in immunocompromised individuals. Double auxotrophic mutants of Mtb lacking the ability to synthesize leucine and pantothenate are safe and sterilized in immunocompromised mice and SIV-infected Rhesus macaques. We examined how immunization with a Mtb triple auxotrophic strain, mc 2 7902, which cannot synthesize leucine, pantothenate, and arginine, protects immunocompetent mice from a virulent Mtb infection. The route of immunization was a crucial factor for protection with mc 2 7902 with intravenous immunization being 100 times more effective in protecting immunocompetent mice from Mtb challenge when compared to conventional subcutaneous vaccination with BCG. To further increase the safety of the attenuated auxotroph for vaccine purposes, the type VII secretion system Esx1 responsible for BCG attenuation was deleted in mc 2 7902. When tested by prime-boost immunization of immunocompetent mice followed by aerosol challenge with virulent Mtb , mc 2 7902 Δ esx1 provided similar protection to mc 2 7902. This robust protection against Mtb infection conferred by mc 2 7902 and mc 2 7902 Δ esx1 in a mouse model paves the way for new TB vaccine development using highly attenuated, auxotrophic Mtb strains.

External validation of the RSNA 2020 pulmonary embolism detection challenge winning deep learning algorithm

PurposeTo evaluate the diagnostic performance and generalizability of the winning DL algorithm of the RSNA 2020 PE detection challenge to a local population using CTPA data from two hospitals. Materials and MethodsConsecutive CTPA images from patients referred for suspected PE were retrospectively analysed. The winning RSNA 2020 DL algorithm was retrained on the RSNA-STR Pulmonary Embolism CT (RSPECT) dataset. The algorithm was tested in hospital A on multidetector CT (MDCT) images of 238 patients and in hospital B on spectral detector CT (SDCT) and virtual monochromatic images (VMI) of 114 patients. The output of the DL algorithm was compared with a reference standard, which included a consensus reading by at least two experienced cardiothoracic radiologists for both hospitals. Areas under the receiver operating characteristic curve (AUCs) were calculated. Sensitivity and specificity were determined using the maximum Youden index. ResultsAccording to the reference standard, PE was present in 73 patients (30.7%) in hospital A and 33 patients (29.0%) in hospital B. For the DL algorithm the AUC was 0.96 (95% CI 0.92–0.98) in hospital A, 0.89 (95% CI 0.81–0.94) for conventional reconstruction in hospital B and 0.87 (95% CI 0.80–0.93) for VMI. ConclusionThe RSNA 2020 pulmonary embolism detection on CTPA challenge winning DL algorithm, retrained on the RSPECT dataset, showed high diagnostic accuracy on MDCT images. A somewhat lower performance was observed on SDCT images, which suggest additional training on novel CT technology may improve generalizability of this DL algorithm.

Robust Immune Response and Protection against Lethal Pneumococcal Challenge with a Recombinant BCG-PspA-PdT Prime/Boost Scheme Administered to Neonatal Mice.

Pneumococcal diseases are an important public health problem, with high mortality rates in young children. Although conjugated pneumococcal vaccines offer high protection against invasive pneumococcal diseases, this is restricted to vaccine serotypes, leading to serotype replacement. Furthermore, the current vaccines do not protect neonates. Therefore, several protein-based pneumococcal vaccines have been studied over the last few decades. Our group established a recombinant BCG expressing rPspA-PdT as a prime/rPspA-PdT boost strategy, which protected adult mice against lethal intranasal pneumococcal challenge. Here, we immunized groups of neonate C57/Bl6 mice (6-10) (at 5 days) with rBCG PspA-PdT and a boost with rPspA-PdT (at 12 days). Controls were saline or each antigen alone. The prime/boost strategy promoted an IgG1 to IgG2c isotype shift compared to protein alone. Furthermore, there was an increase in specific memory cells (T and B lymphocytes) and higher cytokine production (IFN-γ, IL-17, TNF-α, IL-10, and IL-6). Immunization with rBCG PspA-PdT/rPspA-PdT showed 100% protection against pulmonary challenge with the WU2 pneumococcal strain; two doses of rPspA-PdT showed non-significant protection in the neonates. These results demonstrate that a prime/boost strategy using rBCG PspA-PdT/rPspA-PdT is effective in protecting neonates against lethal pneumococcal infection via the induction of strong antibody and cytokine responses.

Cannabidiol Reduces Systemic Immune Activation in Experimental Acute Lung Injury.

Background: The underlying pathomechanism of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is the immune response to inflammation or infection within the pulmonary microcirculation. Systemic spread of pathogens, activated immune cells, and inflammatory mediators contributes significantly to mortality in patients with ARDS. Objective: The endogenous cannabinoid system is a major modulator of the immune response during inflammation and infection. Phytocannabinoids, such as cannabidiol (CBD), have shown promising anti-inflammatory effects in several pathologies. The overall objective of this study was to evaluate the effects of CBD on local and systemic inflammation in endotoxin-induced ALI in mice. Materials and Methods: ALI was induced by pulmonary endotoxin challenge. Four groups of male C57BL/6 mice were randomized in this study: control, ALI, ALI with CBD treatment, and control with CBD treatment. Analyses of local and systemic cytokine levels, lung histology, and leukocyte activation as visualized by intravital microscopy of the intestinal and pulmonary microcirculation were performed 6 h following intranasal endotoxin administration. Results: Pulmonary endotoxin challenge induced significant inflammation evidenced by local and systemic cytokine and chemokine release, lung histopathology, and leukocyte adhesion. Intraperitoneal CBD treatment resulted in a significant decrease in systemic inflammation as shown by reduced leukocyte adhesion in the intestinal microcirculation and reduced plasma cytokine and chemokine levels. Pulmonary chemokine levels were decreased, while pulmonary cytokine levels were unchanged. Surprisingly, the ALI score was slightly increased by CBD treatment in a manner driven by enhanced neutrophil infiltration of the alveoli. Conclusion: In this model of experimental ALI, CBD administration was associated with reduced systemic inflammation and heterogeneous effects on pulmonary inflammation. Future studies should explore the mechanisms involved as they relate to neutrophil infiltration and proinflammatory mediator production within the lungs.

A broadly immunogenic polyvalent Shigella multiepitope fusion antigen protein protects against Shigella sonnei and Shigella flexneri lethal pulmonary challenges in mice.

There are no licensed vaccines for Shigella, a leading cause of children's diarrhea and a common etiology of travelers' diarrhea. To develop a cross-protective Shigella vaccine, in this study, we constructed a polyvalent protein immunogen to present conserved immunodominant epitopes of Shigella invasion plasmid antigens B (IpaB) and D (IpaD), VirG, GuaB, and Shiga toxins on backbone protein IpaD, by applying an epitope- and structure-based multiepitope-fusion-antigen (MEFA) vaccinology platform, examined protein (Shigella MEFA) broad immunogenicity, and evaluated antibody function against Shigella invasion and Shiga toxin cytotoxicity but also protection against Shigella lethal challenge. Mice intramuscularly immunized with Shigella MEFA protein developed IgG responses to IpaB, IpaD, VirG, GuaB, and Shiga toxins 1 and 2; mouse sera significantly reduced invasion of Shigella sonnei, Shigella flexneri serotype 2a, 3a, or 6, Shigella boydii, and Shigella dysenteriae type 1 and neutralized cytotoxicity of Shiga toxins of Shigella and Shiga toxin-producing Escherichia coli in vitro. Moreover, mice intranasally immunized with Shigella MEFA protein (adjuvanted with dmLT) developed antigen-specific serum IgG, lung IgG and IgA, and fecal IgA antibodies, and survived from lethal pulmonary challenge with S. sonnei or S. flexneri serotype 2a, 3a, or 6. In contrast, the control mice died, became unresponsive, or lost 20% of body weight in 48 h. These results indicated that this Shigella MEFA protein is broadly immunogenic, induces broadly functional antibodies, and cross-protects against lethal pulmonary challenges with S. sonnei or S. flexneri serotypes, suggesting a potential application of this polyvalent MEFA protein in Shigella vaccine development.

Acyloxyacyl hydrolase promotes pulmonary defense by preventing alveolar macrophage tolerance.

Although alveolar macrophages (AMs) play important roles in preventing and eliminating pulmonary infections, little is known about their regulation in healthy animals. Since exposure to LPS often renders cells hyporesponsive to subsequent LPS exposures ("tolerant"), we tested the hypothesis that LPS produced in the intestine reaches the lungs and stimulates AMs, rendering them tolerant. We found that resting AMs were more likely to be tolerant in mice lacking acyloxyacyl hydrolase (AOAH), the host lipase that degrades and inactivates LPS; isolated Aoah-/- AMs were less responsive to LPS stimulation and less phagocytic than were Aoah+/+ AMs. Upon innate stimulation in the airways, Aoah-/- mice had reduced epithelium- and macrophage-derived chemokine/cytokine production. Aoah-/- mice also developed greater and more prolonged loss of body weight and higher bacterial burdens after pulmonary challenge with Pseudomonas aeruginosa than did wildtype mice. We also found that bloodborne or intrarectally-administered LPS desensitized ("tolerized") AMs while antimicrobial drug treatment that reduced intestinal commensal Gram-negative bacterial abundance largely restored the innate responsiveness of Aoah-/- AMs. Confirming the role of LPS stimulation, the absence of TLR4 prevented Aoah-/- AM tolerance. We conclude that commensal LPSs may stimulate and desensitize (tolerize) alveolar macrophages in a TLR4-dependent manner and compromise pulmonary immunity. By inactivating LPS in the intestine, AOAH promotes antibacterial host defenses in the lung.

NADPH oxidase 2 limits amplification of IL-1β-G-CSF axis and animmature neutrophil subset in murine lung inflammation.

The leukocyte NADPH oxidase 2 (NOX2) regulates inflammation independent of its antimicrobial activity. Inherited defects in NOX2 lead to chronic granulomatous disease (CGD), associated with recurrent bacterial and fungal infections, often with excessive neutrophilic inflammation that results in significant inflammatory burden and tissue damage. We previously showed that excessive leukotriene B4 (LTB4) production by NOX2-deficient mouse neutrophils was a key driver of elevated lung neutrophil infiltration in the initial response to pulmonary challenge with the model fungal particle zymosan. We now identify interleukin-1β (IL-1β) and downstream granulocyte colony-stimulating factor (G-CSF) as critical amplifying signals that augment and sustain neutrophil accrual in CGD mice. Neutrophils, delivered into the lung via LTB4, were the primary source of IL-1β within the airways, and their increased numbers in CGD lungs led to significantly elevated local and plasma G-CSF. Elevated G-CSF simultaneously promoted increased granulopoiesis and mobilized the release of higher numbers of an immature CD101- neutrophil subset from the marrow, which trafficked to the lung and acquired a significantly more proinflammatory transcriptome in CGD mice compared with wild-type mice. Thus, neutrophil-produced IL-1β and downstream G-CSF act sequentially but nonredundantly with LTB4 to deploy neutrophils and amplify inflammation in CGD mice after inhalation of zymosan. NOX2 plays a critical role in dampening multiple components of a feed-forward pipeline for neutrophil recruitment, and these findings highlight NOX2 as a key regulator of neutrophil number, subsets, and function at inflamed sites.

Rapid Induction of Protective Immunity against Pneumonic Plague by Yersinia pestis Polymeric F1 and LcrV Antigens

In a recent study, we demonstrated that vaccination with the polymeric F1 capsule antigen of the plague pathogen Yersinia pestis led to the rapid induction of a protective humoral immune response via the pivotal activation of innate-like B1b cells. Conversely, the monomeric version of F1 failed to promptly protect vaccinated animals in this model of the bubonic plague. In this study, we examined the ability of F1 to confer the rapid onset of protective immunity in the more challenging mouse model of the pneumonic plague. Vaccination with one dose of F1 adsorbed on aluminum hydroxide elicited effective protection against subsequent lethal intranasal exposure to a fully virulent Y. pestis strain within a week. Interestingly, the addition of the LcrV antigen shortened the time required for achieving such rapid protective immunity to 4-5 days after vaccination. As found previously, the polymeric structure of F1 was essential in affording the accelerated protective response observed by covaccination with LcrV. Finally, in a longevity study, a single vaccination with polymeric F1 induced a higher and more uniform humoral response than a similar vaccination with monomeric F1. However, in this setting, the dominant contribution of LcrV to long-lasting immunity against a lethal pulmonary challenge was reiterated.

IoMT-Enabled Computer-Aided Diagnosis of Pulmonary Embolism from Computed Tomography Scans Using Deep Learning.

The Internet of Medical Things (IoMT) has revolutionized Ambient Assisted Living (AAL) by interconnecting smart medical devices. These devices generate a large amount of data without human intervention. Learning-based sophisticated models are required to extract meaningful information from this massive surge of data. In this context, Deep Neural Network (DNN) has been proven to be a powerful tool for disease detection. Pulmonary Embolism (PE) is considered the leading cause of death disease, with a death toll of 180,000 per year in the US alone. It appears due to a blood clot in pulmonary arteries, which blocks the blood supply to the lungs or a part of the lung. An early diagnosis and treatment of PE could reduce the mortality rate. Doctors and radiologists prefer Computed Tomography (CT) scans as a first-hand tool, which contain 200 to 300 images of a single study for diagnosis. Most of the time, it becomes difficult for a doctor and radiologist to maintain concentration going through all the scans and giving the correct diagnosis, resulting in a misdiagnosis or false diagnosis. Given this, there is a need for an automatic Computer-Aided Diagnosis (CAD) system to assist doctors and radiologists in decision-making. To develop such a system, in this paper, we proposed a deep learning framework based on DenseNet201 to classify PE into nine classes in CT scans. We utilized DenseNet201 as a feature extractor and customized fully connected decision-making layers. The model was trained on the Radiological Society of North America (RSNA)-Pulmonary Embolism Detection Challenge (2020) Kaggle dataset and achieved promising results of 88%, 88%, 89%, and 90% in terms of the accuracy, sensitivity, specificity, and Area Under the Curve (AUC), respectively.

Cross attention guided multi-scale feature fusion for false-positive reduction in pulmonary nodule detection

False-positive reduction is a crucial step of computer-aided diagnosis (CAD) system for pulmonary nodules detection and it plays an important role in lung cancer diagnosis. In this paper, we propose a novel cross attention guided multi-scale feature fusion method for false-positive reduction in pulmonary nodule detection. Specifically, a 3D SENet50 fed with a candidate nodule cube is applied as the backbone to acquire multi-scale coarse features. Then, the coarse features are refined and fused by the multi-scale fusion part to achieve a better feature extraction result. Finally, a 3D spatial pyramid pooling module is used to enhance receptive field and a distributed aligned linear classifier is applied to get the confidence score. In addition, each of the five nodule cubes with different sizes centering on every testing nodule position is fed into the proposed framework to obtain a confidence score separately and a weighted fusion method is used to improve the generalization performance of the model. Extensive experiments are conducted to demonstrate the effectiveness of the classification performance of the proposed model. The data used in our work is from the LUNA16 pulmonary nodule detection challenge. In this data set, the number of true-positive pulmonary nodules is 1,557, while the number of false-positive ones is 753,418. The new method is evaluated on the LUNA16 dataset and achieves the score of the competitive performance metric (CPM) 84.8%.

Live mucosal vaccination stimulates potent protection via varied CD4+ and CD8+ T cell subsets against wild-type Brucella melitensis 16M challenge.

Re-emerging zoonotic pathogen Brucella spp. continues to impact developing countries and persists in expanding populations of wildlife species in the US, constantly threatening infection of our domestic herds. The development of improved animal and human vaccines remains a priority. In this study, immunity to a novel live attenuated B. melitensis strain, termed znBM-mC, was characterized. An oral prime, intranasal (IN) boost strategy conferred exquisite protection against pulmonary challenge, with wild-type (wt) B. melitensis providing nearly complete protection in the lungs and spleens from brucellae colonization. Vaccination with znBM-mC showed an IFN-γ+ CD8+ T-cell bias in the lungs as opposed to Rev 1-vaccinated mice showing IFN-γ+ CD4+ T-cell inclination. Lung CD4+ and CD8+ effector memory T cells (TEMs) increased over 200-fold; and lung CD4+ and CD8+ resident memory T cells (TRMs) increased more than 250- and 150-fold, respectively. These T cells served as the primary producers of IFN-γ in the lungs, which was essential for vaccine clearance and the predominant cytokine generated pre-and post-challenge with wt B. melitensis 16M; znBM-mC growth could not be arrested in IFN-γ−/− mice. Increases in lung TNF-α and IL-17 were also induced, with IL-17 being mostly derived from CD4+ T cells. Vaccination of CD4−/−, CD8−/−, and B6 mice with znBM-mC conferred full protection in the lungs and spleens post-pulmonary challenge with virulent B. melitensis; vaccination of IL-17−/− mice resulted in the protection of the lungs, but not the spleen. These data demonstrate the efficacy of mucosal vaccine administration for the generation of protective memory T cells against wt B. melitensis.

Whole-cell vaccine candidates induce a protective response against virulent Acinetobacter baumannii.

Acinetobacter baumannii causes multi-system diseases in both nosocomial settings and a pre-disposed general population. The bacterium is not only desiccation-resistant but also notoriously resistant to multiple antibiotics and drugs of last resort including carbapenem, colistin, and sulbactam. The World Health Organization has categorized carbapenem-resistant A. baumannii at the top of its critical pathogen list in a bid to direct urgent countermeasure development. Several early-stage vaccines have shown a range of efficacies in healthy mice, but no vaccine candidates have advanced into clinical trials. Herein, we report our findings that both an ionizing γ-radiation-inactivated and a non-ionizing ultraviolet C-inactivated whole-cell vaccine candidate protects neutropenic mice from pulmonary challenge with virulent AB5075, a particularly pathogenic isolate. In addition, we demonstrate that a humoral response is sufficient for this protection via the passive immunization of neutropenic mice.

Batf3-dependent regulation of the antifungal inflammatory response after pulmonary Aspergillus fumigatus challenge

Abstract Aspergillus fumigatus is a ubiquitous fungus that causes invasive aspergillosis in immunocompromised individuals. The innate immune system is critical in the maintenance of host resistance against A. fumigatus. While it is well established that monocyte-derived dendritic cells (moDC) are critical in maintaining host resistance against A. fumigatus, the role of other dendritic cells populations has not been thoroughly explored. Here we demonstrate that Batf3-dependent cells, likely classical type 1 dendritic cells (cDC1s), are critical in preventing invasive aspergillosis. Surprisingly, Batf3(−/−) mice display an elevated inflammatory response against A. fumigatus, particularly IL-17A/F. We show that elevated concentrations of IL-17A/F in the lungs of Batf3(−/−) mice following A. fumigatus infection perpetuates the secretion of various inflammatory lung cytokines in vivo. Neutralization of both IL-17A and IL-17F in Batf3(−/−) mice prevent excessive cytokine secretion and mortality due to A. fumigatus challenge of Batf3(−/−) mice. Following A. fumigatus challenge regulatory T cells are known to limit inflammation. Our preliminary antibody-mediated depletion studies demonstrate that CD4+ CD25+ T cells may be involved in preventing excessive IL-17A/F release in immunocompetent mice. In this study we have identified a critical role for Batf3-dependent cells in limiting A. fumigatus induced inflammatory and mortality due to IL-17 driven lung pathology. Supported by NIH: [R01 AI139133-01A1]

The Age-Driven Decline in Neutrophil Function Contributes to the Reduced Efficacy of the Pneumococcal Conjugate Vaccine in Old Hosts.

Despite the availability of vaccines, Streptococcus pneumoniae (pneumococcus) remains a serious cause of infections in the elderly. The efficacy of anti-pneumococcal vaccines declines with age. While age-driven changes in antibody responses are well defined, less is known about the role of innate immune cells such as polymorphonuclear leukocytes (PMNs) in the reduced vaccine protection seen in aging. Here we explored the role of PMNs in protection against S. pneumoniae in vaccinated hosts. We found that depletion of PMNs in pneumococcal conjugate vaccine (PCV) treated young mice prior to pulmonary challenge with S. pneumoniae resulted in dramatic loss of host protection against infection. Immunization boosted the ability of PMNs to kill S. pneumoniae and this was dependent on bacterial opsonization by antibodies. Bacterial opsonization with immune sera increased several PMN anti-microbial activities including bacterial uptake, degranulation and ROS production. As expected, PCV failed to protect old mice against S. pneumoniae. In probing the role of PMNs in this impaired protection, we found that aging was accompanied by an intrinsic decline in PMN function. PMNs from old mice failed to effectively kill S. pneumoniae even when the bacteria were opsonized with immune sera from young controls. In exploring mechanisms, we found that PMNs from old mice produced less of the antimicrobial peptide CRAMP and failed to efficiently kill engulfed pneumococci. Importantly, adoptive transfer of PMNs from young mice reversed the susceptibility of vaccinated old mice to pneumococcal infection. Overall, this study demonstrates that the age-driven decline in PMN function impairs vaccine-mediated protection against Streptococcus pneumoniae.