SOCS3 regulates pathological retinal angiogenesis through modulating SPP1 expression in microglia and macrophages.

Pathological ocular angiogenesis has long been associated with myeloid cell activation. However, the precise cellular and molecular mechanisms governing the intricate crosstalk between the immune system and vascular changes during ocular neovascularization formation remain elusive. In this study, we demonstrated that the absence of the suppressor of cytokine signaling 3 (SOCS3) in myeloid cells led to a substantial accumulation of microglia and macrophage subsets during the neovascularization process. Our single-cell RNA sequencing data analysis revealed a remarkable increase in the expression of the secreted phosphoprotein 1 (Spp1) gene within these microglia and macrophages, identifying subsets of Spp1-expressing microglia and macrophages during neovascularization formation in angiogenesis mouse models. Notably, the number of Spp1-expressing microglia and macrophages exhibited further elevation during neovascularization in mice lacking myeloid SOCS3. Moreover, our investigation unveiled the Spp1 gene as a direct transcriptional target gene of signal transducer and activator of transcription 3. Importantly, pharmaceutical activation of SOCS3 or blocking of SPP1 resulted in a significant reduction in pathological neovascularization. In conclusion, our study highlights the pivotal role of the SOCS3/STAT3/SPP1 axis in the regulation of pathological retinal angiogenesis.

OSCAA: A two-dimensional Gaussian mixture model for copy number variation association analysis.

Copy number variants (CNVs) are prevalent in the human genome and are found to have a profound effect on genomic organization and human diseases. Discovering disease-associated CNVs is critical for understanding the pathogenesis of diseases and aiding their diagnosis and treatment. However, traditional methods for assessing the association between CNVs and disease risks adopt a two-stage strategy conducting quantitative CNV measurements first and then testing for association, which may lead to biased association estimation and low statistical power, serving as a major barrier in routine genome-wide assessment of such variation. In this article, we developed One-Stage CNV-disease Association Analysis (OSCAA), a flexible algorithm to discover disease-associated CNVs for both quantitative and qualitative traits. OSCAA employs a two-dimensional Gaussian mixture model that is built upon the PCs from copy number intensities, accounting for technical biases in CNV detection while simultaneously testing for their effect on outcome traits. In OSCAA, CNVs are identified and their associations with disease risk are evaluated simultaneously in a single step, taking into account the uncertainty of CNV identification in the statistical model. Our simulations demonstrated that OSCAA outperformed the existing one-stage method and traditional two-stage methods by yielding a more accurate estimate of the CNV-disease association, especially for short CNVs or CNVs with weak signals. In conclusion, OSCAA is a powerful and flexible approach for CNV association testing with high sensitivity and specificity, which can be easily applied to different traits and clinical risk predictions.

MerTK-dependent efferocytosis by monocytic-MDSCs mediates resolution of post-lung transplant injury.

Rationale: Patients with end stage lung diseases require lung transplantation (LTx) that can be impeded by ischemia-reperfusion injury (IRI) leading to subsequent chronic lung allograft dysfunction (CLAD) and inadequate outcomes. Objectives: We examined the undefined role of MerTK (receptor Mer tyrosine kinase) on monocytic myeloid-derived suppressor cells (M-MDSCs) in efferocytosis (phagocytosis of apoptotic cells) to facilitate resolution of lung IRI. Methods: Single-cell RNA sequencing of lung tissue and BAL from post-LTx patients was analyzed. Murine lung hilar ligation and allogeneic orthotopic LTx models of IRI were used with Balb/c (WT), cebpb -/- (MDSC-deficient), Mertk -/- or MerTK-CR (cleavage resistant) mice. Lung function, IRI (inflammatory cytokine and myeloperoxidase expression, immunohistology for neutrophil infiltration), and flow cytometry of lung tissue for efferocytosis of apoptotic neutrophils were assessed in mice. Measurements and Main Results: A significant downregulation in MerTK-related efferocytosis genes in M-MDSC populations of CLAD patients compared to healthy subjects was observed. In the murine IRI model, significant increase in M-MDSCs, MerTK expression and efferocytosis was observed in WT mice during resolution phase that was absent in cebpb -/- Land Mertk -/- mice. Adoptive transfer of M-MDSCs in cebpb -/- mice significantly attenuated lung dysfunction, and inflammation leading to resolution of IRI. Additionally, in a preclinical murine orthotopic LTx model, increases in M-MDSCs were associated with resolution of lung IRI in the transplant recipients. In vitro studies demonstrated the ability of M-MDSCs to efferocytose apoptotic neutrophils in a MerTK-dependent manner. Conclusions: Our results suggest that MerTK-dependent efferocytosis by M-MDSCs can significantly contribute to the resolution of post-LTx IRI.

A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data.

The availability of single-cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect of mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in SCS data using various clustering methods, as cells comprising a subpopulation are found to share a genetic profile. However, currently available methods may generate spurious results (e.g., falsely identified variants) in the procedure of CNA detection, thereby diminishing the accuracy of subclone identification within a large, complex cell population. In this study, we developed a subclone clustering method based on a fused lasso model, referred to as FLCNA, which can simultaneously detect CNAs in single-cell DNA sequencing (scDNA-seq) data. Spike-in simulations were conducted to evaluate the clustering and CNA detection performance of FLCNA, benchmarking it against existing copy number estimation methods (SCOPE, HMMcopy) in combination with commonly used clustering methods. Application of FLCNA to a scDNA-seq data set of breast cancer revealed different genomic variation patterns in neoadjuvant chemotherapy-treated samples and pretreated samples. We show that FLCNA is a practical and powerful method for subclone identification and CNA detection with scDNA-seq data.

The Effect of Different Diluents and Curing Agents on the Performance of Epoxy Resin-Based Intumescent Flame-Retardant Coatings.

The epoxy resin-based (ESB) intumescent flame-retardant coatings were modified with 1,4-butanediol diglycidyl ether (14BDDE) and butyl glycidyl ether (BGE) as diluents and T403 and 4,4'-diaminodiphenylmethane (DDM) as curing agents, respectively. The effects of different diluents and curing agents on the flame-retardant and mechanical properties, as well as the composition evolution of the coatings, were investigated by using large-plate combustion, the limiting oxygen index (LOI), vertical combustion, a cone calorimeter, X-ray diffraction, FTIR analysis, a N2 adsorption and desorption test, a scanning electron microscope (SEM), a tensile strength test, and a viscosity test. The results showed that the addition of 14BBDE and T403 promoted the oxidation of B4C and the formation of boron-containing glass or ceramics, increased the residual mass of char, densified the surface char layer, and increased the specific surface area of porous residual char. When their dosage was 30%, ESB-1T-3 coating exhibited the most excellent flame-retardant properties. During the 2 h large-plate combustion test, the backside temperature was only 138.72 °C, without any melting pits. In addition, the peak heat release rate (PHRR), total heat release rate (THR), total smoke production (TSP), and peak smoke production (PSPR) were reduced by 13.15%, 13.9%, 5.48%, and 17.45%, respectively, compared to the blank ESB coating. The LOI value reached 33.4%, and the vertical combustion grade was V-0. In addition, the tensile strength of the ESB-1T-3 sample was increased by 10.94% compared to ESB. In contrast, the addition of BGE and DDM promoted the combustion of the coating, affected the ceramic process of the coating, seriously affected the formation of borosilicate glass, and exhibited poor flame retardancy. The backside temperature reached 190.93 °C after 2 h combustion. A unified rule is that as the amount of diluent and curing agent increases, the flame retardancy improves while the mechanical properties decrease. This work provides data support for the preparation and process optimization of resin-based coatings.

CYP2A6 Activity and Cigarette Consumption Interact in Smoking-Related Lung Cancer Susceptibility.

Cigarette smoke, containing both nicotine and carcinogens, causes lung cancer. However, not all smokers develop lung cancer, highlighting the importance of the interaction between host susceptibility and environmental exposure in tumorigenesis. Here, we aimed to delineate the interaction between metabolizing ability of tobacco carcinogens and smoking intensity in mediating genetic susceptibility to smoking-related lung tumorigenesis. Single-variant and gene-based associations of 43 tobacco carcinogen-metabolizing genes with lung cancer were analyzed using summary statistics and individual-level genetic data, followed by causal inference of Mendelian randomization, mediation analysis, and structural equation modeling. Cigarette smoke-exposed cell models were used to detect gene expression patterns in relation to specific alleles. Data from the International Lung Cancer Consortium (29,266 cases and 56,450 controls) and UK Biobank (2,155 cases and 376,329 controls) indicated that the genetic variant rs56113850 C>T located in intron 4 of CYP2A6 was significantly associated with decreased lung cancer risk among smokers (OR = 0.88, 95% confidence interval = 0.85-0.91, P = 2.18 × 10-16), which might interact (Pinteraction = 0.028) with and partially be mediated (ORindirect = 0.987) by smoking status. Smoking intensity accounted for 82.3% of the effect of CYP2A6 activity on lung cancer risk but entirely mediated the genetic effect of rs56113850. Mechanistically, the rs56113850 T allele rescued the downregulation of CYP2A6 caused by cigarette smoke exposure, potentially through preferential recruitment of transcription factor helicase-like transcription factor. Together, this study provides additional insights into the interplay between host susceptibility and carcinogen exposure in smoking-related lung tumorigenesis. SIGNIFICANCE: The causal pathway connecting CYP2A6 genetic variability and activity, cigarette consumption, and lung cancer susceptibility in smokers highlights the need for behavior modification interventions based on host susceptibility for cancer prevention.

Migraine and major depression: localizing shared genetic susceptibility in different cell types of the nervous systems.

Background: There is a bidirectional relationship between migraine and major depression disorder (MDD). They likely share important risk genes associated with different cell types in the central nervous system (CNS) and peripheral nervous system (PNS). Profiling the expression of these genes in specific cell types is critical in understanding the pathophysiology of the relationship between migraine and MDD. Methods: Associated genes shared by migraine and MDD were identified by consolidating multiple curations of human disease-gene associations. Subsequently, the expression of overlapping genes was profiled and compared across the different cell types in CNS, PNS and neurovascular cells using eight single cell RNA sequencing datasets, including two human CNS datasets, two mouse CNS datasets, one human PNS dataset and three mouse PNS datasets. Results: 45 shared genes between migraine and MDD were identified. Consistently found in all eight datasets, dopaminergic and serotonergic neurotransmitters were broadly expressed in CNS and PNS cell types. Glutamatergic and endocannabinoid genes were specifically expressed in CNS neurons and astrocytes. Synthesis and/or Release and Binding of Neuropeptides were specifically expressed in PNS peptidergic nociceptor (PEP). Genes related to inflammatory factors and immune responses were specifically expressed in CNS microglia. Among which, IL1B and COMT were highly expressed in CNS microglia cells. Conclusion: Single cell RNA sequencing of the CNS and PNS helps to identify the shared genes between migraine and MDD that are enriched in specific cell types. The findings provide new insight in understanding the underlying mechanism of action for the bidirectional co-morbidity between migraine and MDD.

Vibrio parahaemolyticus and Vibrio vulnificus in vitro biofilm dispersal from microplastics influenced by simulated human environment.

Growing concerns exist regarding human ingestion of contaminated seafood that contains Vibrio biofilms on microplastics (MPs). One of the mechanisms enhancing biofilm related infections in humans is due to biofilm dispersion, a process that triggers release of bacteria from biofilms into the surrounding environment, such as the gastrointestinal tract of human hosts. Dispersal of cells from biofilms can occur in response to environmental conditions such as sudden changes in temperature, pH and nutrient conditions, as the bacteria leave the biofilm to find a more stable environment to colonize. This study evaluated how brief exposures to nutrient starvation, elevated temperature, different pH levels and simulated human media affect Vibrio parahaemolyticus and Vibrio vulnificus biofilm dispersal and processes on and from low-density polyethylene (LDPE), polypropylene (PP), and polystyrene (PS) MPs. Both species were able to adequately disperse from all types of plastics under most exposure conditions. V. parahaemolyticus was able to tolerate and survive the low pH that resembles the gastric environment compared to V. vulnificus. pH had a significantly (p ≤ 0.05) positive effect on overall V. parahaemolyticus biofilm biomass in microplates and cell colonization from PP and PS. pH also had a positive effect on V. vulnificus cell colonization from LDPE and PP. However, most biofilm biomass, biofilm cell and dispersal cell densities of both species greatly varied after exposure to elevated temperature, pH, and nutrient starvation. It was also found that certain exposures to simulated human media affected both V. parahaemolyticus and V. vulnificus biofilm biomass and biofilm cell densities on LDPE, PP and PS compared to exposure to traditional media of similar pH. Cyclic-di-GMP was higher in biofilm cells compared to dispersal cells, but exposure to more stressful conditions significantly increased signal concentrations in both biofilm and dispersal states. Taken together, this study suggests that human pathogenic strains of V. parahaemolyticus and V. vulnificus can rapidly disperse with high cell densities from different plastic types in vitro. However, the biofilm dispersal process is highly variable, species specific and dependent on plastic type, especially under different human body related environmental exposures.

OSCAA: A Two-Dimensional Gaussian Mixture Model for Copy Number Variation Association Analysis.

Copy number variants (CNVs) are prevalent in the human genome which provide profound effect on genomic organization and human diseases. Discovering disease associated CNVs is critical for understanding the pathogenesis of diseases and aiding their diagnosis and treatment. However, traditional methods for assessing the association between CNVs and disease risks adopt a two-stage strategy conducting quantitative CNV measurements first and then testing for association, which may lead to biased association estimation and low statistical power, serving as a major barrier in routine genome wide assessment of such variation. In this article, we developed OSCAA, a flexible algorithm to discover disease associated CNVs for both quantitative and qualitative traits. OSCAA employs a two-dimensional Gaussian mixture model that is built upon the principal components from copy number intensities, accounting for technical biases in CNV detection while simultaneously testing for their effect on outcome traits. In OSCAA, CNVs are identified and their associations with disease risk are evaluated simultaneously in a single step, taking into account the uncertainty of CNV identification in the statistical model. Our simulations demonstrated that OSCAA outperformed the existing one-stage method and traditional two-stage methods by yielding a more accurate estimate of the CNV-disease association, especially for short CNVs or CNVs with weak signal. In conclusion, OSCAA is a powerful and flexible approach for CNV association testing with high sensitivity and specificity, which can be easily applied to different traits and clinical risk predictions.

A Novel Inorganic Aluminum Phosphate-Based Flame Retardant and Thermal Insulation Coating and Performance Analysis.

Currently, most thin-layer expandable coatings are polymer-based, with very few inorganic expandable coatings. Due to the high environmental friendliness of inorganic coatings, studying new types of inorganic coatings is of great significance. A novel amorphous aluminum phosphate-based flame-retardant coating was prepared by modifying it with nano-silica, hollow silica beads, hollow glass microspheres, and boron carbide. A comprehensive study was conducted on the flame retardancy and thermal insulation performance, composition and structural evolution under flame and physical and chemical properties, and the mechanisms of flame retardancy and thermal insulation were elucidated. Large-plate combustion testing, bonding strength testing, XRD, IR, TG-DSC, and SEM testing were all applied in this work. The synergistic effect of the four fillers was very obvious, and a series of AP22XY (nano-silica/silica beads/hollow glass microspheres/boron carbide = 2:2:0:4, 2:2:1:3, 2:2:2:2, 2:2:3:1, 2:2:4:0) coatings were prepared. The change in the ratio of glass microspheres to boron carbide had a significant impact on the composition and structural evolution of the coating, thus reflecting its effectiveness as a flame retardant and thermal insulation. Although decreasing the ratio would promote the formation of borosilicate glass and Al18B4O33 and improve the thermal stability of coatings, the structure inside of the coating, especially the skeleton, would be dense, which is not conducive to thermal insulation. When the ratio of glass microspheres to boron carbide is 3:1, AP2231 shows the best fire resistance. Under the combustion of butane flame at about 1200-1300 °C, the backside temperature reaches a maximum of 226 °C at 10 min, and then the temperature gradually decreases to 175 °C at 60 min. This excellent performance is mainly attributed to three aspects: (1) the foaming and expandability of coatings when exposed to fire, (2) the multiple endothermic reactions the coating undergoes, and (3) the improvement effect of boron carbide. Additionally, AP2231 shows the best bonding performance with a strength of close to 4.5 MPa after combustion, because of the appropriate content matching between borosilicate glass, Al18B4O33, and hollow glass microspheres. The coating has potential application prospects in the construction and transportation fields, such as the protection of structural steel, fire prevention in subways and tunnels, and the prevention of lithium battery fires.

CDK8 and CDK19: positive regulators of signal-induced transcription and negative regulators of Mediator complex proteins.

We have conducted a detailed transcriptomic, proteomic and phosphoproteomic analysis of CDK8 and its paralog CDK19, alternative enzymatic components of the kinase module associated with transcriptional Mediator complex and implicated in development and diseases. This analysis was performed using genetic modifications of CDK8 and CDK19, selective CDK8/19 small molecule kinase inhibitors and a potent CDK8/19 PROTAC degrader. CDK8/19 inhibition in cells exposed to serum or to agonists of NFκB or protein kinase C (PKC) reduced the induction of signal-responsive genes, indicating a pleiotropic role of Mediator kinases in signal-induced transcriptional reprogramming. CDK8/19 inhibition under basal conditions initially downregulated a small group of genes, most of which were inducible by serum or PKC stimulation. Prolonged CDK8/19 inhibition or mutagenesis upregulated a larger gene set, along with a post-transcriptional increase in the proteins comprising the core Mediator complex and its kinase module. Regulation of both RNA and protein expression required CDK8/19 kinase activities but both enzymes protected their binding partner cyclin C from proteolytic degradation in a kinase-independent manner. Analysis of isogenic cell populations expressing CDK8, CDK19 or their kinase-inactive mutants revealed that CDK8 and CDK19 have the same qualitative effects on protein phosphorylation and gene expression at the RNA and protein levels, whereas differential effects of CDK8 versus CDK19 knockouts were attributable to quantitative differences in their expression and activity rather than different functions.

A statistical learning method for simultaneous copy number estimation and subclone clustering with single cell sequencing data.

The availability of single cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect of mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in SCS data using various clustering methods, since cells comprising a subpopulation are found to share genetic profile. However, currently available methods may generate spurious results (e.g., falsely identified CNAs) in the procedure of CNA detection, hence diminishing the accuracy of subclone identification from a large complex cell population. In this study, we developed a CNA detection method based on a fused lasso model, referred to as FLCNA, which can simultaneously identify subclones in single cell DNA sequencing (scDNA-seq) data. Spike-in simulations were conducted to evaluate the clustering and CNA detection performance of FLCNA benchmarking to existing copy number estimation methods (SCOPE, HMMcopy) in combination with the existing and commonly used clustering methods. Interestingly, application of FLCNA to a real scDNA-seq dataset of breast cancer revealed remarkably different genomic variation patterns in neoadjuvant chemotherapy treated samples and pre-treated samples. We show that FLCNA is a practical and powerful method in subclone identification and CNA detection with scDNA-seq data.

Risks of suicide in migraine, non-migraine headache, back, and neck pain: a systematic review and meta-analysis.

Objective: To conduct a systematic review and meta-analysis on suicidal ideation, attempts, and death in patients with head, neck, and back pain. Method: Search was performed using PubMed, Embase, and Web of Science from the date of the first available article through September 31, 2021. A random effects model was used to estimate the pooled odds ratios (ORs) and 95% confidence intervals (95% CI) for the association between suicidal ideation and/or attempt and head, back/neck pain conditions. Articles describing non-migraine headache disorders and death by suicide were also reviewed but not included in the meta-analysis due to an insufficient number of studies. Results: A total of 20 studies met criteria for systemic review. A total of 186,123 migraine patients and 135,790 of neck/back pain patients from 11 studies were included in the meta-analysis. The meta-analysis showed that the estimated risk of combined suicidal ideation and attempt in migraine [OR 2.49; 95% CI: 2.15-2.89] is greater than that in back/neck pain pain [OR 2.00; 95% CI: 1.63-2.45] compared to non-pain control groups. Risk of suicide ideation/planning is 2 folds higher [OR: 2.03; 95% CI: 1.92-2.16] and risk of suicide attempt is more than 3 folds higher [OR: 3.47; 95% CI: 2.68-4.49] in migraine as compared to healthy controls. Conclusion: There is an elevated risk of suicidal ideation and attempt in both migraine and neck/back pain patients in comparison to healthy controls, and this risk is particularly higher among migraine patients. This study underscores the critical need for suicide prevention in migraine patients.

Integrated multi-omics approach to distinct molecular characterization and classification of early-onset colorectal cancer.

Incidence of early-onset colorectal cancer (EOCRC), defined by a diagnosed age under 50 years, is increasing, but its heterogeneous etiologies that differ from general CRC remain undetermined. We initially characterize the genome, epigenome, transcriptome, and proteome of tumors from 79 patients in a Chinese CRC cohort. Data for an additional 126 EOCRC subjects are obtained from the International Cancer Genome Consortium Chinese cohort and The Cancer Genome Atlas European cohort. We observe that early-onset tumors have a high tumor mutation burden; increased DNA repair features by mutational signature 3 and multi-layer pathway enrichments; strong perturbations at effects of DNA methylation and somatic copy-number alteration on gene expression; and upregulated immune infiltration as hot tumors underlying immunophenotypes. Notably, LMTK3 exhibits ancestral mutation disparity, potentially being a functional modulator and biomarker that drives molecular alterations in EOCRC development and immunotherapies. This integrative omics study provides valuable knowledge for precision oncology of CRC.

BISC: accurate inference of transcriptional bursting kinetics from single-cell transcriptomic data.

Gene expression in mammalian cells is inherently stochastic and mRNAs are synthesized in discrete bursts. Single-cell transcriptomics provides an unprecedented opportunity to explore the transcriptome-wide kinetics of transcriptional bursting. However, current analysis methods provide limited accuracy in bursting inference due to substantial noise inherent to single-cell transcriptomic data. In this study, we developed BISC, a Bayesian method for inferring bursting parameters from single cell transcriptomic data. Based on a beta-gamma-Poisson model, BISC modeled the mean-variance dependency to achieve accurate estimation of bursting parameters from noisy data. Evaluation based on both simulation and real intron sequential RNA fluorescence in situ hybridization data showed improved accuracy and reliability of BISC over existing methods, especially for genes with low expression values. Further application of BISC found bursting frequency but not bursting size was strongly associated with gene expression regulation. Moreover, our analysis provided new mechanistic insights into the functional role of enhancer and superenhancer by modulating both bursting frequency and size. BISC also formulated a downstream framework to identify differential bursting (in frequency and size separately) genes in samples under different conditions. Applying to multiple datasets (a mouse embryonic cell and fibroblast dataset, a human immune cell dataset and a human pancreatic cell dataset), BISC identified known cell-type signature genes that were missed by differential expression analysis, providing additional insights in understanding the cell-specific stochastic gene transcription. Applying to datasets of human lung and colon cancers, BISC successfully detected tumor signature genes based on alterations in bursting kinetics, which illustrates its value in understanding disease development regarding transcriptional bursting. Collectively, BISC provides a new tool for accurately inferring bursting kinetics and detecting differential bursting genes. This study also produced new insights in the role of transcriptional bursting in regulating gene expression, cell identity and tumor progression.

Fire Extinguishing Performance of Chemically Bonded Struvite Ceramic Powder with High Heat-Absorbing and Flame Retardant Properties.

Struvite is a chemically bonded ceramic product in the pipeline of a sewage treatment plant. In order to explore the fire extinguishing potential of struvite, a new type of struvite ultrafine dry powder with excellent performance was prepared by a simple process, and its fire extinguishing performance and mechanism were analyzed in depth. Under the same process conditions, the refinement degree (D50 = 5.132 µm) and the specific surface area (BET = 25.72 m2/g) of ultrafine struvite were larger than those of NH4H2PO4 (D50 = 8.961 µm, BET = 13.64 m2/g), making struvite more suitable for fire extinguishing. Besides, the pyrolysis process of struvite was relatively concentrated and absorbed more heat in a short time. Its heat absorption (458.4 J/mg) was higher than that of NH4H2PO4 (156.4 J/mg). Water, ammonia, and PO· were released during the pyrolysis of struvite, which effectively reduced fire temperature, diluted oxygen concentrations and captured free radicals. At the same time, the final products were magnesium orthophosphate and magnesium pyrophosphate, which formed a dense flame-retardant ceramic layer with good thermal insulation and environmental protection functions. In these cases, the fire extinguishing mechanism of struvite was determined to have three stages: the cooling effect, the asphyxiation effect, and the chemical effect. Correspondingly, the fire extinguishing time of struvite was three seconds faster than that of ammonium phosphate under 0.2 MPa based on the local oil basin test.

BMI-CNV: a Bayesian framework for multiple genotyping platforms detection of copy number variants.

Whole-exome sequencing (WES) enables the detection of copy number variants (CNVs) with high resolution in protein-coding regions. However, variants in the intergenic or intragenic regions are excluded from studies. Fortunately, many of these samples have been previously sequenced by other genotyping platforms which are sparse but cover a wide range of genomic regions, such as SNP array. Moreover, conventional single sample-based methods suffer from a high false discovery rate due to prominent data noise. Therefore, methods for integrating multiple genotyping platforms and multiple samples are highly demanded for improved copy number variant detection. We developed BMI-CNV, a Bayesian Multisample and Integrative CNV (BMI-CNV) profiling method with data sequenced by both whole-exome sequencing and microarray. For the multisample integration, we identify the shared copy number variants regions across samples using a Bayesian probit stick-breaking process model coupled with a Gaussian Mixture model estimation. With extensive simulations, BMI-copy number variant outperformed existing methods with improved accuracy. In the matched data from the 1000 Genomes Project and HapMap project data, BMI-CNV also accurately detected common variants and significantly enlarged the detection spectrum of whole-exome sequencing. Further application to the data from The Research of International Cancer of Lung consortium (TRICL) identified lung cancer risk variant candidates in 17q11.2, 1p36.12, 8q23.1, and 5q22.2 regions.

Breast cancer cell-derived microRNA-155 suppresses tumor progression via enhancing immune cell recruitment and antitumor function.

Evidence suggests that increased microRNA-155 (miR-155) expression in immune cells enhances antitumor immune responses. However, given the reported association of miR-155 with tumorigenesis in various cancers, a debate is provoked on whether miR-155 is oncogenic or tumor suppressive. We aimed to interrogate the impact of tumor miR-155 expression, particularly that of cancer cell-derived miR-155, on antitumor immunity in breast cancer. We performed bioinformatic analysis of human breast cancer databases, murine experiments, and human specimen examination. We revealed that higher tumor miR-155 levels correlate with a favorable antitumor immune profile and better patient outcomes. Murine experiments demonstrated that miR-155 overexpression in breast cancer cells enhanced T cell influx, delayed tumor growth, and sensitized the tumors to immune checkpoint blockade (ICB) therapy. Mechanistically, miR-155 overexpression in breast cancer cells upregulated their CXCL9/10/11 production, which was mediated by SOCS1 inhibition and increased phosphorylated STAT1 (p-STAT1)/p-STAT3 ratios. We further found that serum miR-155 levels in breast cancer patients correlated with tumor miR-155 levels and tumor immune status. Our findings suggest that high serum and tumor miR-155 levels may be a favorable prognostic marker for breast cancer patients and that therapeutic elevation of miR-155 in breast tumors may improve the efficacy of ICB therapy via remodeling the antitumor immune landscape.