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"Liang, Xi"
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Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution
The heterogeneous nature of tumour microenvironment (TME) underlying diverse treatment responses remains unclear in nasopharyngeal carcinoma (NPC). Here, we profile 176,447 cells from 10 NPC tumour-blood pairs, using single-cell transcriptome coupled with T cell receptor sequencing. Our analyses reveal 53 cell subtypes, including tumour-infiltrating CD8
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T, regulatory T (Treg), and dendritic cells (DCs), as well as malignant cells with different Epstein-Barr virus infection status. Trajectory analyses reveal exhausted CD8
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T and immune-suppressive TNFRSF4
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Treg cells in tumours might derive from peripheral CX3CR1
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CD8
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T and naïve Treg cells, respectively. Moreover, we identify immune-regulatory and tolerogenic LAMP3
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DCs. Noteworthily, we observe intensive inter-cell interactions among LAMP3
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DCs, Treg, exhausted CD8
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T, and malignant cells, suggesting potential cross-talks to foster an immune-suppressive niche for the TME. Collectively, our study uncovers the heterogeneity and interacting molecules of the TME in NPC at single-cell resolution, which provide insights into the mechanisms underlying NPC progression and the development of precise therapies for NPC.
Nasopharyngeal carcinoma is a diverse cancer characterised by a heterogeneous microenvironment. Here, the authors use single cell sequencing to analyse the tumour microenvironment in 10 nasopharyngeal carcinoma tumours and identify different cell types including immune-suppressive T regulatory, tolerogenic dendritic, and exhausted CD8 T cells.
Journal Article
التخفيف من حدة الفقر في الصين المعاصرة
استنادا إلى نظرة عامة على أوضاع الفقر، يقدم هذا الكتاب مسار التخفيف من حدة الفقر والتنمية في الصين، ويشرح نموذج التنمية والتخفي من حدة الفقر بخصائص صينية والتمسك بمباديء (سيطرة الحكومة ومشاركة المجتمع والاعتماد على الذات والتنمية الموجهة والتنمية الشاملة) كما يقدم الكتاب تلخيصا شاملا لإنجازات الصين العظيمة وخبراتها الهامة وإسهاماتها الرئيسية في قضية التخفيف من حدة الفقر في العالم، ويعرض بإيجاز نظرات وممارسات التخفيف المستهدف من الفقر في العصر الجديد من أجل توفير مراجع لكسب المعركة ضد الفقر في الصين وقضية التخفيف من حدة الفقر في العالم.
Book
Assessing the impact of ETS trading profit on emission abatements based on firm-level transactions
The EU Emission Trading System (ETS) is the oldest and currently the largest carbon market in the world, but its purpose of stimulating carbon emissions via trading profits remains unexamined. Based on the complete firm-level transaction records of the EU ETS Phases I and II, here we show that the participating firms’ trading profits and their emission abatements are positively correlated, and the correlation becomes stronger in Phase II than Phase I. Specifically, we observe that non-linearity exists in the correlation; higher firm-level emission abatements can realize larger trading profits. This pattern affects the market fairness, though it may be helpful to incentivise emission abatements. The correlation is more regulated in Phase II than it is in Phase I, thereby indicating that the Phase II is more mature. We also observe that the state-level abatements are largely driven by industrial giants.
Carbon emission trading is an important market-based policy instrument to reduce GHG emission using reward-punishment mechanism. Here the authors show that the EU emission trading schemes operate at its designed purpose and there is a positive and linear relationship between firm profits and the firms’ efforts in abatement.
Journal Article
Ancient Demographics Determine the Effectiveness of Genetic Purging in Endangered Lizards
Abstract
The purging of deleterious alleles has been hypothesized to mitigate inbreeding depression, but its effectiveness in endangered species remains debatable. To understand how deleterious alleles are purged during population contractions, we analyzed genomes of the endangered Chinese crocodile lizard (Shinisaurus crocodilurus), which is the only surviving species of its family and currently isolated into small populations. Population genomic analyses revealed four genetically distinct conservation units and sharp declines in both effective population size and genetic diversity. By comparing the relative genetic load across populations and conducting genomic simulations, we discovered that seriously deleterious alleles were effectively purged during population contractions in this relict species, although inbreeding generally enhanced the genetic burden. However, despite with the initial purging, our simulations also predicted that seriously deleterious alleles will gradually accumulate under prolonged bottlenecking. Therefore, we emphasize the importance of maintaining a minimum population capacity and increasing the functional genetic diversity in conservation efforts to preserve populations of the crocodile lizard and other endangered species.
Journal Article
A TGF‐β signaling‐related lncRNA signature for prediction of glioma prognosis, immune microenvironment, and immunotherapy response
Aims The dysregulation of TGF‐β signaling is a crucial pathophysiological process in tumorigenesis and progression. LncRNAs have diverse biological functions and are significant participants in the regulation of tumor signaling pathways. However, the clinical value of lncRNAs related to TGF‐β signaling in glioma is currently unclear. Methods Data on glioma's RNA‐seq transcriptome, somatic mutation, DNA methylation data, and clinicopathological information were derived from the CGGA and TCGA databases. A prognostic lncRNA signature was constructed by Cox and LASSO regression analyses. TIMER2.0 database was utilized to deduce immune infiltration characteristics. “ELMER v.2” was used to reconstruct TF‐methylation‐gene regulatory network. Immunotherapy and chemotherapy response predictions were implemented by the TIDE algorithm and GDSC database, respectively. In vitro and in vivo experiments were conducted to verify the results and clarify the regulatory mechanism of lncRNA. Results In glioma, a TGF‐β signaling‐related 15‐lncRNA signature was constructed, including AC010173.1, HOXA‐AS2, AC074286.1, AL592424.1, DRAIC, HOXC13‐AS, AC007938.1, AC010729.1, AC013472.3, AC093895.1, AC131097.4, AL606970.4, HOXC‐AS1, AGAP2‐AS1, and AC002456.1. This signature proved to be a reliable prognostic tool, with high risk indicating an unfavorable prognosis and being linked to malignant clinicopathological and genomic mutation traits. Risk levels were associated with different immune infiltration landscapes, where high risk was indicative of high levels of macrophage infiltration. In addition, high risk also suggested better immunotherapy and chemotherapy response. cg05987823 was an important methylation site in glioma progression, and AP‐1 transcription factor family participated in the regulation of signature lncRNA expression. AGAP2‐AS1 knockdown in in vitro and in vivo experiments inhibited the proliferation, migration, and invasion of glioma cells, as well as the growth of glioma, by downregulating the expression levels of NF‐κB and ERK 1/2 in the TGF‐β signaling pathway. Conclusions A prognostic lncRNA signature of TGF‐β signaling was established in glioma, which can be used for prognostic judgment, immune infiltration status inference, and immunotherapy response prediction. AGAP2‐AS1 plays an important role in glioma progression. A TGF‐β signaling‐related lncRNA signature has been established in glioma, which can be used for prognostic judgment, immune infiltration status speculation, and immunotherapy response prediction. Furthermore, in vitro experiments confirmed that silencing of TGF‐β signaling‐related lncRNA could inhibit the proliferation of glioma cells. This study provides candidate biomarkers with clinical application value for glioma.
Journal Article
Numerical analysis of the slipstream development around a high-speed train in a double-track tunnel
Analysis of the slipstream development around the high-speed trains in tunnels would provide references for assessing the transient gust loads on trackside workers and trackside furniture in tunnels. This paper focuses on the computational analysis of the slipstream caused by high-speed trains passing through double-track tunnels with a cross-sectional area of 100 m2. Three-dimensional unsteady compressible Reynolds-averaged Navier-Stokes equations and a realizable k-ε turbulence model were used to describe the airflow characteristics around a high-speed train in the tunnel. The moving boundary problem was treated using the sliding mesh technology. Three cases were simulated in this paper, including two tunnel lengths and two different configurations of the train. The train speed in these three cases was 250 km/h. The accuracy of the numerical method was validated by the experimental data from full-scale tests, and reasonable consistency was obtained. The results show that the flow field around the high-speed trains can be divided into three distinct regions: the region in front of the train nose, the annular region and the wake region. The slipstream development along the two sides of train is not in balance and offsets to the narrow side in the double-track tunnels. Due to the piston effect, the slipstream has a larger peak value in the tunnel than in open air. The tunnel length, train length and length ratio affect the slipstream velocities; in particular, the velocities increase with longer trains. Moreover, the propagation of pressure waves also induces the slipstream fluctuations: substantial velocity fluctuations mainly occur in front of the train, and weaken with the decrease in amplitude of the pressure wave.
Journal Article
Global supply-chain effects of COVID-19 control measures
Countries have sought to stop the spread of coronavirus disease 2019 (COVID-19) by severely restricting travel and in-person commercial activities. Here, we analyse the supply-chain effects of a set of idealized lockdown scenarios, using the latest global trade modelling framework. We find that supply-chain losses that are related to initial COVID-19 lockdowns are largely dependent on the number of countries imposing restrictions and that losses are more sensitive to the duration of a lockdown than its strictness. However, a longer containment that can eradicate the disease imposes a smaller loss than shorter ones. Earlier, stricter and shorter lockdowns can minimize overall losses. A ‘go-slow’ approach to lifting restrictions may reduce overall damages if it avoids the need for further lockdowns. Regardless of the strategy, the complexity of global supply chains will magnify losses beyond the direct effects of COVID-19. Thus, pandemic control is a public good that requires collective efforts and support to lower-capacity countries.
Guan et al. analyse the impacts of COVID-19 restrictions on global supply chains. Earlier, stricter and shorter lockdowns can minimize overall losses. A ‘go-slow’ approach to lifting restrictions may reduce overall damages if it avoids the need for further lockdowns.
Journal Article
Chaotic oppositional sine–cosine method for solving global optimization problems
This study proposed an improved sine–cosine algorithm (SCA) for global optimization tasks. The SCA is a meta-heuristic method ground on sine and cosine functions. It has found its application in many fields. However, SCA still has some shortcomings such as weak global search ability and low solution quality. In this study, the chaotic local search strategy and the opposition-based learning strategy are utilized to strengthen the exploration and exploitation capability of the basic SCA, and the improved algorithm is called chaotic oppositional SCA (COSCA). The COSCA was validated on a comprehensive set of 22 benchmark functions from classical 23 functions and CEC2014. Simulation experiments suggest that COSCA’s global optimization ability is significantly improved and superior to other algorithms. Moreover, COSCA is evaluated on three complex engineering problems with constraints. Experimental results show that COSCA can solve such problems more effectively than different algorithms.
Journal Article
Spur Gear Tooth Pitting Propagation Assessment Using Model-based Analysis
Tooth pitting is a common failure mode of a gearbox. Many researchers investigated dynamic properties of a gearbox with localized pitting damage on a single gear tooth. The dynamic properties of a gearbox with pitting distributed over multiple teeth have rarely been investi- gated. In this paper, gear tooth pitting propagation to neighboring teeth is modeled and investigated for a pair of spur gears. Tooth pitting propagation effect on time-vary- ing mesh stiffness, gearbox dynamics and vibration char- acteristics is studied and then fault symptoms are revealed. In addition, the influence of gear mesh damping and environmental noise on gearbox vibration properties is investigated. In the end, 114 statistical features are tested to estimate tooth pitting growth. Statistical features that are insensitive to gear mesh damping and environmental noise are recommended.
Journal Article