APPLICATION OF GEOSTATISTICS IN THE ESTIMATION OF SUJISHAN GRAPHITE DEPOSITS, MONGOLIA

In this paper, the author used mine 3D software to establish the 3D geological model of Sujishan Graphite deposit, and applied geostatistics to estimate the resource, offered references for next exploration and mining. Surpac was used to set up geological database of Sujishan Graphite deposit, topographical DTM, ore body model and grade model, 3D of drilling database, also analysis the spatial grade distribution in reality. Based on geostatistics, drilling samples are composited and statistically analysed and eliminate the impact of outliers. Experimental variograms were constructed for the striking, dipping and vertical directions. Grade and resource are estimated by ordinary kriging. Comparing to the traditional estimation methods, this 3D software gives reliable estimation, which provides references for dynamic management of mine's resource

HYBRID FINITE-DISCRETE ELEMENT MODELLING OF BLAST-INDUCED EXCAVATION DAMAGED ZONE IN THE TOP-HEADING OF DEEP TUNNELS

A hybrid finite-discrete element method (FEM/DEM) is introduced to model the excavation damage zone induced by blast in a deep tunnel. The key components of the hybrid finite-discrete element method, i.e. transition from continuum to discontinuum through fracture and fragmentation, and detonation-induced gas expansion and flow through fracturing rock, are introduced in detail. The stress and crack initiation and propagation of an uniaxial compression test is then modelled by the proposed method and compared with those well documented in literature to calibrate the hybrid FEM/DEM. The modelled stress-loading displacement curve presents a typical failure process of brittle materials. The calibrated method is then used to model the stress and crack initiation and propagation induced by blast for the last step of excavation in a deep tunnel. A separation contour, which connects the borehole through the radial cracks from each borehole, is observed during the excavation process. The newly formed tunnel wall is produced and the main components of excavation damage zone (EDZ) are obtained. Therefore, the proposed treatment has the capabilities of modelling blast-induced EDZ and rock failure process. It is concluded that the hybrid FEM/DEM is a valuable numerical tool for studying excavation damage zone in terms of crack initiation and propagation and stress distribution

Genome-wide analysis of Dof genes and their response to abiotic stress in rose (Rosa chinensis)

Dof (DNA binding with one finger) proteins play important roles in plant development and defense regulatory networks. In the present study, we report a genome-wide analysis of rose Dof genes (RchDof), including phylogenetic inferences, gene structures, chromosomal locations, gene duplications, and expression diversity. A total of 24 full-length RchDof genes were identified in Rosa chinensis, which were assigned to nine distinct subgroups. These RchDof genes were unevenly distributed on rose chromosomes. The genome-scale analysis of synteny indicated that segmental duplication events may have played a major role in the evolution of the RchDof gene family. Analysis of cis-acting elements revealed putative functions of Dofs in rose during development as well as under numerous biotic and abiotic stress conditions. Moreover, the expression profiles derived from qRT-PCR experiments demonstrated distinct expression patterns in various tissues, and gene expression divergence existed among the duplicated RchDof genes, suggesting a fundamentally functional divergence of the duplicated Dof paralogs in rose. The gene expression analysis of RchDofs under drought and salt stress conditions was also performed. The present study offered novel insights into the evolution of RchDofs and can aid in the further functional characterization of its candidate genes

Transcriptome analysis reveals candidate genes for dietary fiber metabolism in Rosa roxburghii fruit grown under different light intensities

The fruit of the perennial rosebush Rosa roxburghii were valued for their high levels of ascorbic acid, superoxide dismutase activity, and cancer preventing effects. The high cellulose and low pectin content of Rosa roxburghii fruit results in an undesirable fibrous texture and hence needs to be addressed. However, little is known about the molecular mechanisms underlying dietary fiber metabolism in this fruit. Here, we report that the contents of cellulose, pectin, and lignin were increased by shading treatments at the maturation stage of fruit development. Under 50% shading, the soluble pectin content increased by 16.39%, which may improve the fruit palatability. However, deeper shading of 100% caused the lignin content to increase by 28.86%, which conversely may lower fruit quality. Based on transcriptome analysis, we identified candidate genes involved in dietary fiber metabolism, including cellulose synthase (CesA) 1, 2, 3, and 5, â-1,4-xylosyltransferase (IRX), arabinosyltransferase (ARAD) 1 and 2, galacturonosyltransferase (GAUT), cellulolytic enzyme (Cx), and pectin methylesterase, in which CesA1, CesA2, CesA3, IRX, ARAD2, and GAUT3 significantly responded to shading and positively correlated with the content of their corresponding component. Furthermore, cinnamyl alcohol dehydrogenase was significantly regulated by shading treatment and positively correlated with increasing lignin concentration. These results may facilitate a better understanding of the molecular mechanisms of dietary fiber metabolism in R. roxburghii fruit under low light conditions and provide a framework for future crop improvement

Overexpression of RrGGP2 and RrDHAR increases ascorbic acid content in tomato

Ascorbic acid (AsA) is the most abundant antioxidant in plants and is an important nutritional index for agricultural products. Some plants, such as Rosa roxburghii Tratt., contain exceptionally high levels of AsA, but are relatively unpalatable. In view of its role in human health, as well as plant growth and development, we examined the effects of two important AsA regulatory genes from R. roxburghii in tomato, with the aim of producing a crop of higher nutritional quality. RrGGP2 and RrDHAR were cloned from R. roxburghii fruit. The overexpression vectors were made using 35S promoters and mediated by Agrobacterium tumefaciens to obtain the overexpression lines. A PCR and qRT-PCR verified that the two genes had been inserted and overexpressed in the tomato leaves and fruits. The results showed that the overexpression of RrGGP2 increased tomato leaf and fruit AsA content by 108.5% and 294.3%, respectively, while the overexpression of RrDHAR increased tomato leaf and fruit AsA content by 183.9% and 179.9%. The overexpression of RrGGP2 and RrDHAR further changed the expression of genes related to AsA metabolism, and the upregulation of one such gene, SlGGP, may have contributed greatly to the increase in AsA. Results here indicate that RrGGP2 contributes more towards fruit AsA accumulation in tomato than RrDHAR

Gene expression profiling in Rosa roxburghii fruit and overexpressing RrGGP2 in tobacco and tomato indicates the key control point of AsA biosynthesis

Rosa roxburghii Tratt. is an important commercial horticultural crop endemic to China, which is recognized for its extremely high content of L-ascorbic acid (AsA). To understand the mechanisms underlying AsA overproduction in fruit of R. roxburghii, content levels, accumulation rate, and the expression of genes putatively in the biosynthesis of AsA during fruit development have been characterized. The content of AsA increased with fruit weight during development, and AsA accumulation rate was found to be highest between 60 and 90 days after anthesis (DAA), with approximately 60% of the total amount being accumulated during this period. In vitro incubating analysis of 70DAA fruit flesh tissues confirmed that AsA was synthesized mainly via the L-galactose pathway although L-Gulono-1, 4-lactone was also an effective precursor elevating AsA biosynthesis. Furthermore, in transcript level, AsA content was significantly associated with GDP-L-galactose phosphorylase (RrGGP2) gene expression. Virus-induced RrGGP2 silencing reduced the AsA content in R. roxburghii fruit by 28.9%. Overexpressing RrGGP2 increased AsA content by 8-12-fold in tobacco leaves and 2.33-3.11-fold in tomato fruit, respectively, and it showed enhanced resistance to oxidative stress caused by paraquat in transformed tobacco. These results further justified the importance of RrGGP2 as a major control step to AsA biosynthesis in R. roxburghii fruit

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

A multimodal cell census and atlas of the mammalian primary motor cortex

ABSTRACT We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties