Ovarian cancer has the highest mortality rate among gynecological malignant tumors, and it preferentially metastasizes to omental tissue, leading to intestinal obstruction and death. scRNA-seq is a ...powerful technique to reveal tumor heterogeneity. Analyzing omentum metastasis of ovarian cancer at the single-cell level may be more conducive to exploring and understanding omentum metastasis and prognosis of ovarian cancer at the cellular function and genetic levels.
The omentum metastasis site scRNA-seq data of GSE147082 were acquired from the GEO (Gene Expression Omnibus) database, and single cells were clustered by the Seruat package and annotated by the SingleR package. Cell differentiation trajectories were reconstructed through the monocle package. The ovarian cancer microarray data of GSE132342 were downloaded from GEO and were clustered by using the ConsensusClusterPlus package into omentum metastasis-associated clusters according to the marker genes gained from single-cell differentiation trajectory analysis. The tumor microenvironment (TME) and immune infiltration differences between clusters were analyzed by the estimate and CIBERSORT packages. The expression matrix of genes used to cluster GSE132342 patients was extracted from bulk RNA-seq data of TCGA-OV (The Cancer Genome Atlas ovarian cancer), and least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression were performed to establish an omentum metastasis-associated gene (OMAG) signature. The signature was then tested by GSE132342 data. Finally, the clinicopathological characteristics of TCGA-OV were screened by univariate and multivariate Cox regression analysis to draw the nomogram.
A total of 9885 cells from 6 patients were clustered into 18 cell clusters and annotated into 14 cell types. Reconstruction of differentiation trajectories divided the cells into 5 branches, and a total of 781 cell trajectory-related characteristic genes were obtained. A total of 3769 patients in GSE132342 were subtyped into 3 clusters by 74 cell trajectory-related characteristic genes. Kaplan-Meier (K-M) survival analysis showed that the prognosis of cluster 2 was the worst, P < 0.001. The TME analysis showed that the ESTIMATE score and stromal score in cluster 2 were significantly higher than those in the other two clusters, P < 0.001. The immune infiltration analysis showed differences in the fraction of 8 immune cells among the 3 clusters, P < 0.05. The expression data of 74 genes used for GEO clustering were extracted from 379 patients in TCGA-OV, and combined with survival information, 10 candidates for OMAGs were filtered by LASSO. By using multivariate Cox regression, the 6-OMAGs signature was established as RiskScore = 0.307*TIMP3 + 3.516*FBN1-0.109*IGKC + 0.209*RPL21 + 0.870*UCHL1 + 0.365*RARRES1. Taking TCGA-OV as the training set and GSE132342 as the test set, receiver operating characteristic (ROC) curves were drawn to verify the prognostic value of 6-OMAGs. Screened by univariate and multivariate Cox regression analysis, 3 (age, cancer status, primary therapy outcome) of 5 clinicopathological characteristics were used to construct the nomogram combined with risk score.
We constructed an ovarian cancer prognostic model related to omentum metastasis composed of 6-OMAGs and 3 clinicopathological features and analyzed the potential mechanism of these 6-OMAGs in ovarian cancer omental metastasis.
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Abstract
A calm astronomical site means a site where astronomical observation would be less likely to be interfered with by optical turbulence. Previous turbulence measurements at a few sites in ...Antarctica have demonstrated very calm atmospheric conditions here. So far, to realize a wide range of measurements of the turbulence conditions above the Antarctic plateau will be a great hardship. Thus, in this study, the numerical weather model outputs provided by the Antarctic Mesoscale Prediction System (AMPS) have been used. Based on the AMPS outputs, the boundary layer height and the atmospheric Richardson number were obtained, from which the turbulence conditions above the Antarctic plateau have been evaluated. Finally, a statistical conclusion evaluating the total atmospheric turbulence above the whole Antarctic continent for an entire year is first reported. We find some sites (or regions) have a calmer atmosphere than Dome A; this is of great instructional significance for planning the next generation of ground-based optical astronomical telescopes.
Amyloid precursor protein (APP) processing is central in Alzheimer's disease (AD) pathogenesis. The healthy unaffected neurons suffer the transmission of amyloid protein from pathologically affected ...neurons, which may play an important role in the anatomical spread of the disease. Exosomes are appropriate candidates for transmission of amyloid species, because of their potential role as “intercellular transportation”. To address a role of secreted exosomes in neuronal homeostasis in AD, we harvested exosomes from the conditioned medium of HEK293-APP Swe/Ind cells. We have demonstrated that these exosomes contained APP and were capable of efficiently transferring APP to normal primary neurons. Moreover, these exosomes had dose-dependent detrimental effect on cultured neurons. Our results suggest a key mechanism underlying the spread of amyloid protein in the brain and the acceleration of pathology in AD; exosomes secretion serves to amplify and propagate Alzheimer's disease related pathology.
•Exosomes secreted from HEK-APP Swe/Ind cells contain flAPP and P-APP.•These exosomes show neurotoxic effects and induce neuronal aggregation.•Exosomes can mediate the cell-to-cell transmission of flAPP and P-APP.•High concentration of exosomes that contain APP protein could promote them to be taken by neurons.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Given the multiple roles of associated microbiota in improving animal host fitness in a microbial environment, increasing numbers of researchers have focused on how the associated microbiota keeps ...stable under complex environmental factors, especially some biological ones. Recent studies show that associated microbiota interacts with pathogenic microbes. However, whether and how the interaction would influence microbiota stability is limitedly investigated. Based on the interaction among
Delia antiqua
, its associated microbiota, and one pathogen
Beauveria bassiana
, the associated microbiota's response to the pathogen was determined in this study. Besides, the underlying mechanism for the response was also preliminarily investigated. Results showed that
B. bassiana
neither infect
D. antiqua
larvae nor did it colonize inside the associated microbiota, and both the bacterial and fungal microbiota kept stable during the interaction. Further experiments showed that bacterial microbiota almost completely inhibited conidial germination and mycelial growth of
B. bassiana
during its invasion, while fungal microbiota did not inhibit conidial germination and mycelial growth of
B. bassiana
. According to the above results, individual dominant bacterial species were isolated, and their inhibition on conidial germination and mycelial growth of
B. bassiana
was reconfirmed. Thus, these results indicated that bacterial instead of fungal microbiota blocked
B. bassiana
conidia and stabilized the associated microbiota of
D. antiqua
larvae during
B. bassiana
invasion. The findings deepened the understanding of the role of associated microbiota–pathogen microbe interaction in maintaining microbiota stability. They may also contribute to the development of novel biological control agents and pest management strategies.
Residential coal combustion is considered to be an important source of air pollution in Beijing. However, knowledge regarding the emission characteristics of residential coal combustion and the ...related impacts on the air quality is very limited. In this study, we have developed an emission inventory for multiple hazardous air pollutants (HAPs) associated with residential coal combustion in Beijing for the period of 2000–2012. Furthermore, a widely used regional air quality model, the Community Multi-Scale Air Quality model (CMAQ), is applied to analyze the impact of residential coal combustion on the air quality in Beijing in 2012. The results show that the emissions of primary air pollutants from residential coal combustion have basically remained the same levels during the past decade, however, along with the strict emission control imposed on major industrial sources, the contribution of residential coal combustion emissions to the overall emissions from anthropogenic sources have increased obviously. In particular, the contributions of residential coal combustion to the total air pollutants concentrations of PM10, SO2, NOX, and CO represent approximately 11.6%, 27.5%, 2.8% and 7.3%, respectively, during the winter heating season. In terms of impact on the spatial variation patterns, the distributions of the pollutants concentrations are similar to the distribution of the associated primary HAPs emissions, which are highly concentrated in the rural-urban fringe zones and rural suburb areas. In addition, emissions of primary pollutants from residential coal combustion are forecasted by using a scenario analysis. Generally, comprehensive measures must be taken to control residential coal combustion in Beijing. The best way to reduce the associated emissions from residential coal combustion is to use economic incentive means to promote the conversion to clean energy sources for residential heating and cooking. In areas with reliable energy supplies, the coal used for residential heating can be replaced with gas-burning wall-heaters, ground-source heat pumps, solar energy and electricity. In areas with inadequate clean energy sources, low-sulfur coal should be used instead of the traditional raw coal with high sulfur and ash content, thereby slightly reducing the emissions of PM, SO2, CO and other toxic pollutants.
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•A comprehensive emission inventory of HAPs from coal stoves of Beijing is developed.•Temporal trend of historical period 2000–2012 and the future till 2030 is assessed.•Spatial characteristics of primary air pollutants emissions in 2012 are presented.•Contribution to the atmospheric pollution from residential coal stoves is simulated.•Replacing coal stove with clean energy is critical to improve air quality in winter.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
The fractional entrainment rate in convective clouds is an important parameter in current convective parameterization schemes of climate models. In this paper, it is estimated using a 1-km-resolution ...cloud-resolving model (CRM) simulation of convective clouds from TWP-ICE (the Tropical Warm Pool-International Cloud Experiment). The clouds are divided into different types, characterized by cloud-top heights. The entrainment rates and moist static energy that is entrained or detrained are determined by analyzing the budget of moist static energy for each cloud type. Results show that the entrained air is a mixture of approximately equal amount of cloud air and environmental air, and the detrained air is a mixture of ~80 % of cloud air and 20 % of the air with saturation moist static energy at the environmental temperature. After taking into account the difference in moist static energy between the entrained air and the mean environment, the estimated fractional entrainment rate is much larger than those used in current convective parameterization schemes. High-resolution (100 m) large-eddy simulation of TWP-ICE convection was also analyzed to support the CRM results. It is shown that the characteristics of entrainment rates estimated using both the high-resolution data and CRM-resolution coarse-grained data are similar. For each cloud category, the entrainment rate is high near cloud base and top, but low in the middle of clouds. The entrainment rates are best fitted to the inverse of in-cloud vertical velocity by a second order polynomial.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, SIK, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Platinum-based chemotherapy is one of the most common treatments for many cancers; however, the effect of chemotherapy varies from individual to individual. Excision repair cross complementation ...group 1 (ERCC1) is widely recognized as a key gene regulating nucleotide excision repair (NER) and is closely associated with platinum response. Many studies have yielded conflicting results regarding whether ERCC1 polymorphisms can affect the response to platinum and overall survival (OS). Therefore, it is necessary to perform a meta-analysis of patients with specific races and cancer types.
Eight databases (EMBASE, PubMed, Cochrane Library, Chinese National Knowledge Infrastructure, Scopus, VIP, China Biology Medicine disc and Wanfang databases) were searched. Results were expressed in terms of odds ratios (ORs), hazard ratios (HRs) and 95% CIs.
In this study, rs11615, rs2298881 and rs3212986 SNPs were studied. In the comparison between CT and TT on the response to platinum, esophageal cancer I2 = 0%, OR = 6.18, 95% CI(1.89,20.23), P = 0.003 and ovarian cancer I2 = 0%, OR = 4.94, 95% CI(2.21,11.04), P<0.001 showed that the rs11615 CT genotype predicted a better response. In the comparison between CC and TT, ovarian cancer I2 = 48.0%, OR = 6.15, 95% CI (2.56,14.29), P<0.001 indicated that the CC genotype predicted a better response. In the meta-analysis of OS, the CC genotype was related to longer OS than TT in ovarian cancer TT vs CC: I2 = 57.7%, HR = 1.71, 95% CI (1.18, 2.49), P<0.001.
The ERCC1 rs11615 polymorphism was related to the response to platinum and OS, but the correlation is based on specific cancer types in the Asian population.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Long non-coding RNAs (lncRNAs), a type of epigenetic regulator, are thought to play important roles in embryonic development in mice, and several developmental defects are associated with epigenetic ...modification disorders. The most dramatic epigenetic reprogramming event occurs during somatic cell nuclear transfer (SCNT) when the expression profile of a differentiated cell is abolished, and a newly embryo-specific expression profile is established. However, the molecular mechanism underlying somatic reprogramming remains unclear, and the dynamics and functions of lncRNAs in this process have not yet been illustrated, resulting in inefficient reprogramming.
In this study, 63 single-cell RNA-seq libraries were first generated and sequenced. A total of 7009 mouse polyadenylation lncRNAs (including 5204 novel lncRNAs) were obtained, and a comprehensive analysis of in vivo and SCNT mouse pre-implantation embryo lncRNAs was further performed based on our single-cell RNA sequencing data. Expression profile analysis revealed that lncRNAs were expressed in a developmental stage-specific manner during mouse early-stage embryonic development, whereas a more temporal and spatially specific expression pattern was identified in mouse SCNT embryos with changes in the state of chromatin during somatic cell reprogramming, leading to incomplete zygotic genome activation, oocyte to embryo transition and 2-cell to 4-cell transition. No obvious differences between other stages and mouse NTC or NTM embryos at the same stage were observed. Gene oncology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and weighted gene co-expression network analysis (WGCNA) of lncRNAs and their association with known protein-coding genes suggested that several lncRNAs and their associated with known protein-coding genes might be involved in mouse embryonic development and cell reprogramming.
This is a novel report on the expression landscapes of lncRNAs of mouse NT embryos by scRNA-seq analysis. This study will provide insight into the molecular mechanism underlying the involvement of lncRNAs in mouse pre-implantation embryonic development and epigenetic reprogramming in mammalian species after SCNT-based cloning.
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The Chinese Bohai Sea is a semi-enclosed, highly vulnerable continental sea that is exposed to the risk of oil spills due to offshore oil and gas activities. In this study, a geographic information ...system (GIS)-based “tanks–pipelines–platforms–ships–channels” (TPPSC) comprehensive framework, including a storage tank indicator, a pipeline indicator, a platform indicator, a ship indicator, and a channel indicator, was built to analyze the comprehensive marine oil spill risk in the Bohai Sea and to show the spatial differentiation of risk using GIS and the entropy weight method (EWM). The proposed method will overcome the shortcomings of the traditional statistical and scenario analysis theories. The results show that extremely high-risk areas are mostly located in Liaodong Bay and Bohai Bay; high-risk areas are located in the Bohai Strait and on the north side of the Shandong Peninsula; moderate-risk areas are mainly located on both sides of the Bohai Strait; low-risk areas are located on the south side of Liaodong Bay, in the middle of the Bohai Strait, and in Laizhou Bay; and extremely low-risk areas are located on the west side of Bohai Bay, the south side of Laizhou Bay, and the middle of the Bohai Sea. This framework demonstrated the applicability of the new risk assessment model, and the evaluation tests provided useful information for future research on marine oil spill risk management.
The high elevation, complex topography, and unique atmospheric circulations of the Tibetan Plateau (TP) make its optical turbulence characteristics different from those in low-elevation regions. In ...this study, the characteristics of the atmospheric refractive index structure constant (Cn2) profiles in the Lhasa area at different strength states of the Asian summer monsoon anticyclone (ASMA) are analyzed based on precious in situ sounding data measured over the Lhasa in August 2018. Cn2 in the upper troposphere–lower stratosphere fluctuates significantly within a few days during the ASMA, particularly in the upper troposphere. The effect of the ASMA on Cn2 varies among the upper troposphere, tropopause, and lower stratosphere. The stronger and closer the ASMA is to Lhasa, the more pronounced is the “upper highs and lower lows” pressure field structure, which is beneficial for decreasing the potential temperature lapse rate. The decrease in static stability is an important condition for developing optical turbulence, elevating the tropopause height, and reducing the tropopause temperature. However, if strong high-pressure activity occurs at the lower pressure layer, such as at 500 hPa, an “upper highs and lower highs” pressure field structure forms over the Lhasa, increasing the potential temperature lapse rate and suppressing the convective intensity. Being almost unaffected by low-level atmospheric high-pressure activities, the ASMA, as the main influencing factor, mainly inhibits Cn2 in the tropopause and lower stratosphere. The variations of turbulence intensity in UTLS caused by ASMA activities also have a great influence on astronomical parameters, which will have certain guiding significance for astronomical site testing and observations.
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