Cutting Edge: Negative Regulation of Inflammasome Activation by TRAF1 Can Limit Gout.

Secretion of IL-1ß, a potent cytokine that plays a key role in gout pathogenesis, is regulated by inflammasomes. TRAF1 has been linked to heightened risk to inflammatory arthritis. In this article, we show that TRAF1 negatively regulates inflammasome activation to limit caspase-1 and IL-1ß secretion in human and mouse macrophages. TRAF1 reduces linear ubiquitination and subsequent oligomerization of the adapter protein, ASC. i.p. injection of monosodium urate crystals resulted in increased inflammatory cell infiltrates and IL-1ß production in Traf1 knockout mice compared with wild type littermates. In a model of monosodium urate crystal-induced gout, Traf1 knockout mice exhibited more swelling in the knee joints, increased infiltration of inflammatory cells, and higher expression of proinflammatory cytokines. In summary, this study identifies TRAF1 as a key regulator of IL-1ß production and a potential therapeutic target for inflammasome-driven diseases such as gout.

Post COVID-19 pulmonary complications in outpatient setting: Insights from a cross-sectional study in a rural academic hospital.

OBJECTIVE: Post COVID-19 disease pulmonary complications are generally expected among the hospitalized or elderly patients with multiple comorbidities given the gravity of the disease among such patients. However, non-hospitalized patients with less severe symptoms from COVID-19 disease have also been experiencing significant morbidity and difficulty functioning their activities of daily living. Therefore, we aim to characterize post COVID-19 pulmonary complications (symptomatology, clinical and radiological findings) in patients who did not require hospitalization but had significant outpatient visits secondary to COVID-19 sequelae. METHODS: This is a two part cross-sectional study based on a retrospective chart review. Patients with COVID-19 disease not requiring hospitalization but followed up at pulmonology clinic with respiratory symptoms were analyzed twice in an interval of 12 months. 23 patients in first cross-section group (followed up from December 2019 to June 2021) and 53 patients in second group (followed up from June 2021 to July 2022) were included in the analyses. Differences in mean and percentage of baseline characteristics and clinical outcomes between the two groups are analyzed using unpaired t-tests and Chi-squared tests respectively. Post COVID-19 disease symptoms are classified in to 3 different groups (mild, moderate and severe) based on duration of symptoms and presence or absence of hypoxia. RESULTS: Dyspnea on exertion (DOE) was the common compliant in majority of patients in both cross-section groups (43.5% vs 56.6%). Mean age in years were 33 and 50 in first and second cross-section groups respectively. Majority of the patients had mild and moderate symptoms in both groups (43.5% vs 9.4%, P = 0.0007; 43.5% vs 83%, P = 0.005). Mean duration of symptoms in first cross-section group was 3.8 whereas 10.5 months (P = 0.0001) in second cross-section group. CONCLUSION: Our study outlines the burden of post COVID-19 disease pulmonary complications in patient group where these complications are less expected. Strategies for the implementation of multidisciplinary post COVID-19 care clinic along with mass vaccination awareness campaigns in rural US should be prioritized to mitigate this existing burden.

Physical activity phenotypes and mortality in older adults: a novel distributional data analysis of accelerometry in the NHANES.

Physical activity is deemed critical to successful ageing. Despite evidence and progress, there is still a need to determine more precisely the direction, magnitude, intensity, and volume of physical activity that should be performed on a daily basis to effectively promote the health of individuals. This study aimed to assess the clinical validity of new physical activity phenotypes derived from a novel distributional functional analysis of accelerometer data in older adults. A random sample of participants aged between 65 and 80 years with valid accelerometer data from the National Health and Nutrition Examination Survey (NHANES) 2011-2014 was used. Five major clinical phenotypes were identified, which provided a greater sensitivity for predicting 5-year mortality and survival outcomes than age alone, and our results confirm the importance of moderate-to-vigorous physical activity. The new clinical physical activity phenotypes are a promising tool for improving patient prognosis and for directing to more targeted intervention planning, according to the principles of precision medicine. The use of distributional representations shows clear advantages over more traditional metrics to explore the effects of the full spectrum of the physical activity continuum on human health.

A Principal Neighborhood Aggregation-Based Graph Convolutional Network for Pneumonia Detection.

Pneumonia is one of the main causes of child mortality in the world and has been reported by the World Health Organization (WHO) to be the cause of one-third of child deaths in India. Designing an automated classification system to detect pneumonia has become a worthwhile research topic. Numerous deep learning models have attempted to detect pneumonia by applying convolutional neural networks (CNNs) to X-ray radiographs, as they are essentially images and have achieved great performances. However, they failed to capture higher-order feature information of all objects based on the X-ray images because the topology of the X-ray images' dimensions does not always come with some spatially regular locality properties, which makes defining a spatial kernel filter in X-ray images non-trivial. This paper proposes a principal neighborhood aggregation-based graph convolutional network (PNA-GCN) for pneumonia detection. In PNA-GCN, we propose a new graph-based feature construction utilizing the transfer learning technique to extract features and then construct the graph from images. Then, we propose a graph convolutional network with principal neighborhood aggregation. We integrate multiple aggregation functions in a single layer with degree-scalers to capture more effective information in a single layer to exploit the underlying properties of the graph structure. The experimental results show that PNA-GCN can perform best in the pneumonia detection task on a real-world dataset against the state-of-the-art baseline methods.

Systematic study of the stress-responsive Rboh gene family in Nicotiana tabacum: Genome-wide identification, evolution and role in disease resistance.

Plant respiratory burst oxidase homolog (Rboh) gene family encodes the key enzymatic subunits of reactive oxygen species (ROS) production pathways, and play crucial role in plant signaling, development and stress responses. In present work, twenty genes were identified in Nicotiana tabacum Rboh family (NtabRboh) and classified into four phylogenetic groups (I-IV). Fourteen NtabRboh genes were positioned on ten chromosomes (i.e., Ch1, 2, 4, 7-11, 14 and 21), and six scaffolds. Synteny and evolutionary analysis showed that most of the NtabRboh genes have evolved from the genomes of the ancestor species (N. tomentosiformis and N. sylvestris), which afterwards expanded through duplication events. The promoter regions of the NtabRboh genes contained numerous cis-acting regulatory elements for hormones, plant growth, and different biotic and abiotic factors. The NtabRbohF gene transcript comprised target sites for wounding and stress responsive microRNAs: nta-miR166a-d, g and h. The transcript abundance of NtabRboh genes in different tissues reflected their important for plant growth and organ development in tobacco. RT-qPCR-assays demonstrated that the expression of NtabRboh genes are regulated by viral and bacterial pathogens, drought, cold and cadmium stress. The expression levels NtabRbohA, B and C were significantly up-regulated in "black shank and tobacco mosaic virus-inoculated susceptible and transgenic tobacco cultivars, showing that these genes play important roles in disease resistance.

Diffusion and spillover effects of an evidence-based mental health intervention among peers and caregivers of high risk youth in Sierra Leone: study protocol.

BACKGROUND: Evidence-based mental health interventions have helped address health services gaps, but their reach and societal benefit can be limited in low resource settings. The current study extends an ongoing scale-up study of a cognitive behavioral therapy (CBT)-based intervention, the Youth Readiness Intervention (YRI), among high risk youth in post-conflict Sierra Leone to investigate mechanisms of diffusion and spillover effects of the YRI among peers and caregivers of youth who receive the intervention. METHODS: We will recruit and enroll YRI index participants and control index participants (ages 18-30). Index participants will complete a standardized ego-network survey to nominate three peers in their social networks and identify their primary cohabitating caregiver. Identified peers and caregivers who consent to participate will complete a quantitative assessment battery on mental health outcomes, emotion regulation, and daily functioning at baseline and 8-month follow-up. Study outcomes also incorporate common indicators for implementation science, including measures of project context, evaluation, and scaleup. Social network analysis will investigate diffusion of YRI components across peer networks. Linear growth modeling will examine mental health spillover effects among caregivers. Incremental health costs and benefits among YRI participants' caregivers and peers will be assessed through cost-effectiveness and return on investment analysis. DISCUSSION: Assessing implementation research outcomes, including penetration of YRI effects across social networks and cost-effectiveness of the YRI as distinct outcomes, will provide key information about the success of YRI implementation. Lessons learned could inform decisions to increase scale up efforts in Sub-Saharan Africa and other low resource settings.

Replacing the Guaiac Fecal Occult Blood Test With the Fecal Immunochemical Test Increases Proportion of Individuals Screened in a Large Healthcare Setting.

BACKGROUND & AIMS: The most commonly used noninvasive test for colorectal cancer (CRC) screening has been the guaiac fecal occult blood test (gFOBT). The fecal immunochemical test (FIT) detects CRC and colorectal polyps with higher levels of sensitivity than the gFOBT, and may be more acceptable to patients. However, the FIT has not replaced the gFOBT in many clinical settings. We analyzed data from a large healthcare system that replaced the gFOBT with the FIT to determine the effects on CRC screening. METHODS: We conducted a retrospective observational study of 7898 patients at the Veterans' Administration San Diego Healthcare System, 50-75 years old, who were offered stool-based CRC screening as part of primary care March 2014 through January 2015. Test orders and results were extracted from electronic health records; we performed manual reviews of colonoscopy and pathology reports for Veterans with positive results from the tests. Our primary outcome was test completion within 1 year of order; secondary outcomes were positive results and detection of advanced neoplasia by diagnostic colonoscopy. The primary analysis used an intention-to-screen approach, which included all patients with test orders; as-screened analyses were also performed. RESULTS: Among 7898 patients, 3236 had gFOBT and 4662 FIT orders. In the intention to screen analysis, a significantly higher proportion of subjects completed a FIT (42.6%) than a gFOBT (33.4%) (P < .001); advanced neoplasia was detected in a significantly higher proportion of subjects offered a FIT (0.79%) than a gFOBT (0.28%) (P = .003). The numbers needed to invite to achieve 1 additional completed test and identify 1 additional patient with advanced neoplasia were 11 and 196, respectively. CONCLUSIONS: In a retrospective study of patients at a Veterans' administration healthcare system, replacing the gFOBT with the FIT increased the proportion of patients who completed CRC screening. Replacement of the gFOBT with the FIT should be strongly considered by all healthcare systems.

Pulmonary Chlamydia muridarum challenge activates lung interstitial macrophages which correlate with IFN-γ production and infection control in mice.

Protective immunity to the pathogen Chlamydia is dependent on a robust IFN-γ response generated by innate and adaptive lymphocytes. Here we assess the role of the macrophage in orchestrating a protective response in vivo to the murine pathogen, Chlamydia muridarum. During acute pulmonary and peritoneal infection, resident macrophages in both sites are infected with C. muridarum and adopt an inflammatory phenotype. In the lung, this activation is restricted to interstitial macrophages, which harbor higher levels of C. muridarum 16sRNA than alveolar macrophages. We examined innate and adaptive lymphocyte activation in the peritoneal cavity with macrophage depletion and with adoptive transfer of infected macrophages. These experiments demonstrate macrophage activation correlates with a protective IFN-γ response and effective control of C. muridarum. These studies suggest that a quantitative or qualitative alteration in macrophages may play a key role in the development of Chlamydia-associated diseases.

HLA-B27, but not HLA-B7, immunodominance to influenza is ERAP dependent.

Endoplasmic reticulum-associated aminopeptidase-1 (ERAP1) plays a critical role in the processing of peptides prior to binding to MHC class I molecules. In this article, we show for the first time, to our knowledge, that the HLA-B27 immunodominant influenza nucleoprotein (NP) 383-391 epitope is made as an N-terminally extended 14-mer before it is trimmed by ERAP. In the absence of ERAP, there is a significant reduction in the CTL response to the B27/NP383-391 epitope in influenza A (flu)-infected B27/ERAP(-/-) mice. With the use of tetramer staining, the number of naive CD8(+) T cells expressing TCR Vß8.1 in B27/ERAP(-/-) transgenic mice is significantly lower than that seen in B27/ERAP(+/+) mice. HLA-B27 surface expression in naive and flu-infected B27/ERAP(-/-) mice is also lower than the expression seen for the same allele in naive and flu-infected B27/ERAP(+/+) mice. In contrast, surface expression of HLA-B7 was unaffected by the absence of ERAP in B7/ERAP(-/-) transgenic mice. The B7-restricted NP418-426 CTL response in flu-infected B7/ERAP(-/-) and B7/ERAP(+/+) mice was also similar. These results provide, to our knowledge, the first in vivo demonstration of ERAP functionally influencing host immune response in an HLA allele-specific manner. This principle has relevance to diseases such as ankylosing spondylitis, in which HLA-B27 and ERAP jointly contribute to disease predisposition.

Co-expression of HLA-B7 and HLA-B27 alleles is associated with B7-restricted immunodominant responses following influenza infection.

It is recognized that host response following viral infection is characterized by immunodominance, but deciphering the different factors contributing to immunodominance has proved a challenge due to concurrent expression of multiple MHC class I alleles. To address this, we generated H2-K(-/-)/D(-/-) double-knockout transgenic mice expressing either one or two human MHC-I alleles. We hypothesized that co-expression of different allele combinations figures critically in immunodominance and examined this in influenza-infected, double Tg MHC-I mice. In A2/B7 or A2/B27 mice, using ELISpot assays with the A2-restricted matrix I.58-66, the B7-restricted NP418-426 or the B27-restricted NP383-391 influenza A (flu) epitopes, we observed the expected recognition of both peptides for both alleles. In contrast, in flu-infected B7/B27 mice, a significantly reduced level of B27/NP383-restricted CTL response was detected while there was no change in the B7/NP418-restricted CTL response. Flu-specific tetramer studies revealed a partial deletion of Vß8.1(+) NP383/B27-restricted CD8(+) T cells, and a diminished Vß12(+) CD8(+) T-cell expansion in B7/B27 Tg mice. Using HLA Tg chimeric mice, we confirmed these findings. These findings shed light on the immune consequences of co-dominant expression of MHC-I alleles for host immune response to pathogens.

Fully bio-based epoxy resins from lignin and epoxidized soybean oil: Rigid-flexible, tunable properties and high lignin content.

The application of epoxidized soybean oil (ESO) in thermosetting polymers is impeded by its unsatisfactory thermomechanical properties. Here, in order to address the limitation, technical lignin was modified by tung oil anhydride and then used as the hardener to compensate for the inherent flexibility defects of ESO thermosets (TLs). As the lignin content increased, a notable improvement in the activation energy of TLs was observed, attributed to the restraining effect of lignin's rigid structure on segmental relaxation. Concurrently, the tensile strength of TLs increased from 2.8 MPa to 34.0 MPa, concomitant with a decrease in elongation at break from 32.9 % to 8.0 %. Comparative analysis with TL-0 (devoid of lignin) demonstrated substantial enhancements in glass transition temperature, shape fixation ratio, and shape recovery ratio for TL-50 (comprising 50 wt% of lignin), elevating from 16.9 °C, 89.1 %, and 89.5 % to 118.6 °C, 94.0 %, and 99.3 %, respectively. These results unequivocally highlight the favorable dynamic mechanical and shape memory properties conferred upon TLs by lignin addition. While the introduction of lignin adversely affected thermal stability, a notable improvement in char yield (800 °C) was observed. Collectively, these findings underscore the potential of technical lignin as a promising bio-based curing agent for ESO.

Applications-oriented algicidal efficacy research and in-depth mechanism of a novel strain Brevibacillus sp. on Microcystis aeruginosa.

The utilization of algicidal bacteria for the control of harmful algal blooms (HABs) is a promising technology for ecological remediation. In our most recent publication, a novel strain of Brevibacillus sp. was isolated and proved to have significant algicidal activity and stability against Microcystis aeruginosa. In order to verify the algicidal effect of the strain in the practical application scenario, the algicidal efficacy of Brevibacillus sp. under conditions close to water in the environment was investigated. Results indicated that the algicidal threshold of Brevibacillus sp. culture was 3‰ inoculation concentration, and the removal rate of M. aeruginosa reached 100%. The process of Chl-a degradation followed a first-order kinetic model, which could be used to predict the degradation effect of M. aeruginosa in practical applications. Additionally, the inoculation of Brevibacillus sp. culture introduced additional nutrients, some of which remained in the water. Furthermore, the algicidal substances demonstrated good sustainability, with a removal rate of up to 78.53% at 144 h after three repeated uses. At 12 h, the algicidal substances caused a 78.65% increase in malondialdehyde (MDA) content in M. aeruginosa compared to the control group, thereby triggering the antioxidant system of M. aeruginosa. Moreover, algal cell fragments were observed to aggregate. This study provides a promising direction for treating cyanobacterial blooms using algicidal bacteria in practical applications.

Immunodominance: a pivotal principle in host response to viral infections.

We encounter pathogens on a daily basis and our immune system has evolved to mount an immune response following an infection. An interesting phenomenon that has evolved in response to clearing bacterial and viral infections is called immunodominance. Immunodominance refers to the phenomenon that, despite co-expression of multiple major histocompatibility complex class I alleles by host cells and the potential generation of hundreds of distinct antigenic peptides for recognition following an infection, a large portion of the anti-viral cytotoxic T lymphocyte population targets only some peptide/MHC class I complexes. Here we review the main factors contributing to immunodominance in relation to influenza A and HIV infection. Of special interest are the factors contributing to immunodominance in humans and rodents following influenza A infection. By critically reviewing these findings, we hope to improve understanding of the challenges facing the discovery of new factors enabling better anti-viral vaccine strategies in the future.

Neuroimmune regulation of ventilator-induced lung injury.

RATIONALE: Ventilator-induced lung injury (VILI) contributes to the mortality in patients with acute lung injury by increasing inflammation. Recent evidence suggests that stimulation of the cholinergic antiinflammatory pathway may be an attractive way to attenuate inflammatory injury. OBJECTIVES: To determine the role of vagus nerve signaling in VILI and establish whether stimulation of the vagus reflex can mitigate VILI. METHODS: We performed bilateral vagotomy in a mouse model of high-tidal volume-induced lung injury. We performed pharmacological and electrical vagus nerve stimulation in a rat model of VILI following ischemia/reperfusion injury. To determine the contribution of the alpha 7 acetylcholine nicotinic receptor to pulmonary cell injury, we exposed human bronchial epithelial cells to cyclic stretch in the presence of specific agonist or antagonist of the alpha 7 receptor. MEASUREMENTS AND MAIN RESULTS: Vagotomy exacerbates lung injury from VILI in mice as demonstrated by increased wet-to-dry ratio, infiltration of neutrophils, and increased IL-6. Vagal stimulation attenuates lung injury in rats after ischemia/reperfusion injury ventilated with high-volume strategies. Treatment of both mice and rats with the vagus mimetic drug semapimod resulted in decreased lung injury. Vagotomy also increased pulmonary apoptosis, whereas vagus stimulation (electrical and pharmacological) attenuated VILI-induced apoptosis. In vitro studies suggest that vagus-dependent effects on inflammation and apoptosis are mediated via the α7 nicotinc acetylcholine receptor-dependent effects on cyclic stretch-dependent signaling pathways c-jun N-terminal kinase and tumor necrosis factor receptor superfamily, member 6. CONCLUSIONS: Stimulation of the cholinergic antiinflammatory reflex may represent a promising alternative for the treatment of VILI.

Detection of ASC Oligomerization by Western Blotting.

Apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) is an adaptor protein that is essential for the activation of several inflammasome complexes. Activation of inflammasomes leads to pathogenic clearance and inflammatory cell death called pyroptosis. Upon inflammasome activation, ASC oligomerization leads to the recruitment and activation of caspase-1, which in turn converts pro-inflammatory cytokines (e.g., pro-IL-1ß, pro-IL-18) to their mature active form. Given its central role in inflammasome activation, ASC oligomerization is used as an indicator of inflammasome activation. Here we describe how ASC oligomerization can be detected by Western blotting.

Fast Support Vector Classification for Large-Scale Problems.

The support vector machine (SVM) is a very important machine learning algorithm with state-of-the-art performance on many classification problems. However, on large datasets it is very slow and requires much memory. To solve this defficiency, we propose the fast support vector classifier (FSVC) that includes: 1) an efficient closed-form training free of any numerical iterative procedure; 2) a small collection of class prototypes that avoids to store in memory an excessive number of support vectors; and 3) a fast method that selects the spread of the radial basis function kernel directly from data, without classifier execution nor iterative hyper-parameter tuning. The memory requirements of FSVC are very low, spending in average only 6 ·10-7 sec. per pattern, input and class, and processing datasets up to 31 millions of patterns, 30,000 inputs and 131 classes in less than 1.5 hours (less than 3 hours with only 2GB of RAM). In average, the FSVC is 10 times faster, requires 12 times less memory and achieves 4.7 percent more performance than Liblinear, that fails on the 4 largest datasets by lack of memory, being 100 times faster and achieving only 6.7 percent less performance than Libsvm. The time spent by FSVC only depends on the dataset size and thus it can be accurately estimated for new datasets, while Libsvm or Liblinear are much slower on "difficult" datasets, even if they are small. The FSVC adjusts its requirements to the available memory, classifying large datasets in computers with limited memory. Code for the proposed algorithm in the Octave scientific programming language is provided.1.

Comparative genomics and evolutionary analysis of plant CNGCs.

Comparative genomics and computational biology offer powerful research tools for studying evolutionary mechanisms of organisms, and the identification and characterization of conserved/distant genes and gene families. The plant CNGC gene family encodes evolutionary conserved ion channel proteins involved in important signaling pathways and biological functions. The fundamental ideas and standard procedures for genome-wide identification and evolutionary analysis of plant cyclic nucleotide-gated ion channels employing various software, tools, and online servers have been discussed. In particular, this developed method focused on practical procedures involving the comparative analysis of paralogs and orthologs of CNGC genes in different plant species at different levels including phylogenetic analysis, nomenclature and classification, gene structure, molecular protein evolution, and duplication events as mechanisms of gene family expansion and synteny.

Activating transcription factor 3 confers protection against ventilator-induced lung injury.

RATIONALE: Ventilator-induced lung injury (VILI) significantly contributes to mortality in patients with acute respiratory distress syndrome, the most severe form of acute lung injury. Understanding the molecular basis for response to cyclic stretch (CS) and its derangement during high-volume ventilation is of high priority. OBJECTIVES: To identify specific molecular regulators involved in the development of VILI. METHODS: We undertook a comparative examination of cis-regulatory sequences involved in the coordinated expression of CS-responsive genes using microarray analysis. Analysis of stretched versus nonstretched cells identified significant enrichment for genes containing putative binding sites for the transcription factor activating transcription factor 3 (ATF3). To determine the role of ATF3 in vivo, we compared the response of ATF3 gene-deficient mice to wild-type mice in an in vivo model of VILI. MEASUREMENTS AND MAIN RESULTS: ATF3 protein expression and nuclear translocation is increased in the lung after mechanical ventilation in wild-type mice. ATF3-deficient mice have greater sensitivity to mechanical ventilation alone or in conjunction with inhaled endotoxin, as demonstrated by increased cell infiltration and proinflammatory cytokines in the lung and bronchoalveolar lavage, and increased pulmonary edema and indices of tissue injury. The expression of stretch-responsive genes containing putative ATF3 cis-regulatory regions was significantly altered in ATF3-deficient mice. CONCLUSIONS: ATF3 deficiency confers increased sensitivity to mechanical ventilation alone or in combination with inhaled endotoxin. We propose ATF3 acts to counterbalance CS and high volume-induced inflammation, dampening its ability to cause injury and consequently protecting animals from injurious CS.

Solitary Fibrous Tumors of the Pleura.

Solitary fibrous tumors of the pleura (SFTP) are rare neoplasms. We present a case of a 53-year-old female presenting to the pulmonary clinic after an incidental finding of a right-sided chest wall tumor on a chest X-ray. A CT scan of the chest showed a pleural-based right upper lung mass; a biopsy of the mass was consistent with a solitary fibrous tumor.