Genetic Variation and Geographical Differentiation of \u3cem\u3eElymus nutans\u3c/em\u3e (Poaceae: Triticeae) from West China

Elymus nutans Griseb. is not only an important alpine forage grass, but also as a crucial gene pool for improving cereal crops. Understanding and maintaining the genetic diversity of the species are essential for both conservation strategy and breeding programs. However, little is known about its genetic and geographical differentiation patterns. E. nutans is a perennial, caespitose and allohexaploid (2n=6x=42) species that contains the St, H and Y genomes. It is native to temperate and tropical Asia, ranging from western and central Asia in the west to China and Mongolia in the east, from Russia in the north to India and the Himalayas areas in the south (Clayton et al. 2006). It is distributed in the north, northwest and southwest China, particularly in the Qinghai-Tibet Plateau. E. nutans is a valuable forage grass in the alpine regions that is resistant to cold, drought and pests, which can be used to improve cereal crops. In addition, it can play an important role in the restoration of disturbed grasslands and the establishment of artificial grasslands, especially at altitudes from 3,000 to 4,500 m (Chen and Jia 2000). During recent decades, its distribution has contracted because of over-exploitation, habitat destruction and fragmentation. Therefore, it is urgent to understand and monitor the genetic and geographical differentiation of wild germplams of E. nutans

Construction of multi-mineral digital rocks for upscaling the numerical simulation of tight rock physical properties

Tight sandstone reservoirs are characterized by multi-scale pore space and high clay content, resulting in intricate rock physical responses. In this work, multi-scale imaging techniques, including computed tomography and stitched scanning electron microscopy, are applied to identify the large intergranular pores and micropores within major minerals. The pore structure of tight sandstones is quantitatively investigated using multi-scale images. Besides, multi-mineral digital rocks are constructed by performing registration and segmentation processing on the images obtained from microcomputed tomography and energy-dispersive scanning electron microscopy. These digital rocks are treated as composite materials consisting of different mineral types and micro-porosities, which enables the upscaling of the numerical simulation of rock physics properties. The results reveal that residual intergranular pores are interconnected through micropores within clay minerals, which significantly influences the electrical conductivities and permeabilities of tight sandstones. The proposed upscaling method can effectively couple the contribution of formation brine in multi-scale pores and clay minerals to bulk rock physics properties. This approach is suitable for the numerical simulation of diverse rock physical properties and can be applied to various tight reservoirs.Document Type: PerspectiveCited as: Hu, J., Xiao, Z., Ni, H., Liu, X. Construction of multi-mineral digital rocks for upscaling the numerical simulation of tight rock physical properties. Advances in Geo-Energy Research, 2023, 9(1): 68-70. https://doi.org/10.46690/ager.2023.07.0

In silico method for systematic analysis of feature importance in microRNA-mRNA interactions

<p>Abstract</p> <p>Background</p> <p>MicroRNA (miRNA), which is short non-coding RNA, plays a pivotal role in the regulation of many biological processes and affects the stability and/or translation of mRNA. Recently, machine learning algorithms were developed to predict potential miRNA targets. Most of these methods are robust but are not sensitive to redundant or irrelevant features. Despite their good performance, the relative importance of each feature is still unclear. With increasing experimental data becoming available, research interest has shifted from higher prediction performance to uncovering the mechanism of microRNA-mRNA interactions.</p> <p>Results</p> <p>Systematic analysis of sequence, structural and positional features was carried out for two different data sets. The dominant functional features were distinguished from uninformative features in single and hybrid feature sets. Models were developed using only statistically significant sequence, structural and positional features, resulting in area under the receiver operating curves (AUC) values of 0.919, 0.927 and 0.969 for one data set and of 0.926, 0.874 and 0.954 for another data set, respectively. Hybrid models were developed by combining various features and achieved AUC of 0.978 and 0.970 for two different data sets. Functional miRNA information is well reflected in these features, which are expected to be valuable in understanding the mechanism of microRNA-mRNA interactions and in designing experiments.</p> <p>Conclusions</p> <p>Differing from previous approaches, this study focused on systematic analysis of all types of features. Statistically significant features were identified and used to construct models that yield similar accuracy to previous studies in a shorter computation time.</p

Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) play a key role in regulating various biological processes such as participating in the post-transcriptional pathway and affecting the stability and/or the translation of mRNA. Current methods have extracted feature information at different levels, among which the characteristic stem-loop structure makes the greatest contribution to the prediction of putative miRNA precursor (pre-miRNA). We find that none of these features alone is capable of identifying new pre-miRNA accurately.</p> <p>Results</p> <p>In the present work, a pre-miRNA stem-loop secondary structure is translated to a network, which provides a novel perspective for its structural analysis. Network parameters are used to construct prediction model, achieving an area under the receiver operating curves (AUC) value of 0.956. Moreover, by repeating the same method on two independent datasets, accuracies of 0.976 and 0.913 are achieved, respectively.</p> <p>Conclusions</p> <p>Network parameters effectively characterize pre-miRNA secondary structure, which improves our prediction model in both prediction ability and computation efficiency. Additionally, as a complement to feature extraction methods in previous studies, these multifaceted features can reflect natural properties of miRNAs and be used for comprehensive and systematic analysis on miRNA.</p

Evolution of anthropogenic air pollutant emissions in Guangdong Province, China, from 2006 to 2015

Guangdong Province (GD), one of the most prosperous and populous regions in China, still experiences haze events and growing ozone pollution in spite of the substantial air-quality improvement in recent years. Integrated control of fine particulate matter (PM2.5) and ozone in GD calls for a systematic review of historical emissions. In this study, emission trends, spatial variations, source-contribution variations, and reduction potentials of sulfur dioxide (SO2), nitrogen oxides (NO), PM2.5, inhalable particles (PM10), carbon monoxide (CO), ammonia (NH3), and volatile organic compounds (VOCs) in GD from 2006 to 2015 were first examined using a dynamic methodology, taking into account economic development, technology penetration, and emission controls. The relative change rates of anthropogenic emissions in GD during 2006-2015 are -48% for SO2, -0.5% for NO, -16% for PM2.5, -22% for PM10, 13% for CO, 3% for NH3, and 13% for VOCs. The declines of SO2, NO, PM2.5, and PM10 emissions in the whole province mainly resulted from the stringent emission control in the Pearl River delta (PRD) region, where most previous control measures were focused, especially on power plants (SO2 and NO), industrial combustion (SO2, PM2.5, PM10), on-road mobile sources (NO), and dust sources (PM2.5 and PM10). Emissions from other areas (non-PRD, NPRD), nevertheless, remain relatively stable due to the lax control measures and rapidly growing energy consumption. In addition, emission leaks of SO2 and NO from industries are observed from PRD to NPRD in 2010 and 2011. As a result, emissions in NPRD are increasingly important in GD, particularly those from industrial combustion. The contribution of NPRD to the total SO2 emissions in GD, for example, increased from 27% in 2006 to 48% in 2015. On-road mobile sources and solvent use are the two key sources that should receive more effective control measures in GD. Current control-driven emission reductions from on-road mobile sources are neutralized by the substantial growth of the vehicle population, while VOC emissions in GD steadily increase due to the growth of solvent use and the absence of effective control measures. Besides, future work could focus on power plants and industrial combustion in GD and industrial process sources in NPRD, which still have large emission reduction potentials. The historical emission inventory developed in this study not only helps to understand the emission evolution in GD, but also provides robust data to quantify the impact of emission and meteorology variations on air quality and unveil the primary cause of significant air-quality change in GD in the recent decade

Rodent models of postherpetic neuralgia: How far have we reached?

BackgroundInduced by varicella zoster virus (VZV), postherpetic neuralgia (PHN) is one of the common complications of herpes zoster (HZ) with refractory pain. Animal models play pivotal roles in disclosing the pain mechanisms and developing effective treatments. However, only a few rodent models focus on the VZV-associated pain and PHN.ObjectiveTo summarize the establishment and characteristics of popular PHN rodent models, thus offer bases for the selection and improvement of PHN models.DesignIn this review, we retrospect two promising PHN rodent models, VZV-induced PHN model and HSV1-induced PHN model in terms of pain-related evaluations, their contributions to PHN pathogenesis and pharmacology.ResultsSignificant difference of two PHN models is the probability of virus proliferation; 2) Most commonly used pain evaluation of PHN model is mechanical allodynia, but pain-induced anxiety and other behaviours are worth noting; 3) From current PHN models, pain mechanisms involve changes in virus gene and host gene expression, neuroimmune–glia interactions and ion channels; 4) antiviral drugs and classical analgesics serve more on the acute stage of herpetic pain.ConclusionsDifferent PHN models assessed by various pain evaluations combine to fulfil more comprehensive understanding of PHN

Electricity Transmission Strategy Research Based on Wind-Coal-Battery-Hydrogen-CCUS Multi Energy Coupling and Bundling System

[Introduction] In order to guarantee urban power supply and offshore wind power utilization without building new power lines, the paper aims to establish a electricity transmission strategy based on wind-coal-battery- hydrogen -CCUS multi energy coupling and bundling system, which is analyzed theoretically and verified by simulation.[Method] To verify the effectiveness of the strategy, four experimental schemes (separate transmission of wind and coal power, bundled transmission of wind and coal power without operation coupling, bundled transmission of wind and coal power with operation coupling, and wind-coal-battery-hydrogen-CCUS coupled transmission) were set up, and based on the HOMER software environment and particle swarm optimization algorithm, the system operation simulation and index calculation of the test scheme are carried out.[Result] According to the simulation results, compared with normal separate transmission strategy, power transmission line capacity of system applying wind-coal bundled transmission strategy can be decreased by 2.2 GW, with an average utilization rate of 59%, i.e. 21%~23% higher. In the case that the wind power and coal power share the same transmission line without coordinated operation, the wind power curtailment is 164 GWh in total. System applying wind-coal-battery–hydrogen-CCUS bundled transmission strategy could avoid wind power curtailment and reduce carbon emission from unit power supply by about 30~33g/MWh. [Conclusion] In conclusion, the electricity transmission strategy established by this paper is supposed to be feasible and effective and contributing to planning and construction of offshore wind power project

Genotype–Phenotype Analysis of RPGR Variations: Reporting of 62 Chinese Families and a Literature Review

PurposeRPGR is the most common cause of X-linked retinitis pigmentosa (RP), of which female carriers are also frequently affected. The aim of the current study was to explore the RPGR variation spectrum and associated phenotype based on the data from our lab and previous studies.MethodsVariants in RPGR were selected from exome sequencing data of 7,092 probands with different eye conditions. The probands and their available family members underwent comprehensive ocular examinations. Similar data were collected from previous reports through searches in PubMed, Web of Science, and Google Scholar. Systematic analyses of genotypes, phenotypes and their correlations were performed.ResultsA total of 46 likely pathogenic variants, including nine missense and one in-frame variants in RCC1-like domain and 36 truncation variants, in RPGR were detected in 62 unrelated families in our in-house cohort. In addition, a total of 585 variants, including 491 (83.9%) truncation variants, were identified from the literature. Systematic analysis of variants from our in-house dataset, literature, and gnomAD suggested that most of the pathogenic variants of RPGR were truncation variants while pathogenic missense and in-frame variants were enriched in the RCC1-like domain. Phenotypic variations were present between males and female carriers, including more severe refractive error but better best corrected visual acuity (BCVA) in female carriers than those in males. The male patients showed a significant reduction of BCVA with increase of age and males with exon1-14 variants presented a better BCVA than those with ORF15 variants. For female carriers, the BCVA also showed significant reduction with increase of age, but BCVA in females with exon1-14 variants was not significant difference compared with those with ORF15 variants.ConclusionMost pathogenic variants of RPGR are truncations. Missense and in-frame variants located outside of the RCC1-like domain might be benign and the pathogenicity criteria for these variants should be considered with greater caution. The BCVA and refractive error are different between males and female carriers. Increase of age and location of variants in ORF15 contribute to the reduction of BCVA in males. These results are valuable for understanding genotypes and phenotypes of RPGR