Evaluation Index System for Railway Hub Logistics Base System Layout Planning, Taking Hefei Railway Hub in China as an Example

The construction of a railway hub logistics base system has many influencing factors and a high construction cost. There is an extremely important social and economic significance to the evaluation of its planning scheme. This study has obtained practical experience from a large number of existing railway hub planning schemes in China, using the analytic hierarchy process. Then, macro- and micro-level layout planning principles were analyzed. Moreover, 16 evaluation indicators were established at the macro and micro levels. The analytic hierarchy process and a comprehensive evaluation index method were used to deal with all indicators and give the score of the planning scheme. Lastly, Hefei railway hub in China was taken as an example to test the theory above

New advances of DNA methylation in liver fibrosis, with special emphasis on the crosstalk between microRNAs and DNA methylation machinery

AbstractEpigenetics refers to the study of heritable changes in the pattern of gene expression that is controlled by a mechanism specifically not due to changes the primary DNA sequence. Well-known epigenetic mechanisms include DNA methylation, post-translational histone modifications and RNA-based mechanisms including those controlled by small non-coding RNAs (miRNAs). Recent studies have shown that epigenetic modifications orchestrate the hepatic stellate cell (HSC) activation and liver fibrosis. In this review we focus on the aberrant methylation of CpG island promoters of select genes is the prominent epigenetic mechanism to effectively silence gene transcription facilitating HSC activation and liver fibrosis. Furthermore, we also discuss epigenetic dysregulation of tumor-suppressor miRNA genes by promoter DNA methylation and the interaction of DNA methylation with miRNAs involved in the regulation of HSC activation and liver fibrosis. Recent advances in epigenetics alterations in the pathogenesis of liver fibrosis and their possible use as new therapeutic targets and biomarkers

Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute

<p>Abstract</p> <p>Background</p> <p>Increasingly large amounts of DNA sequencing data are being generated within the Wellcome Trust Sanger Institute (WTSI). The traditional file system struggles to handle these increasing amounts of sequence data. A good data management system therefore needs to be implemented and integrated into the current WTSI infrastructure. Such a system enables good management of the IT infrastructure of the sequencing pipeline and allows biologists to track their data.</p> <p>Results</p> <p>We have chosen a data grid system, iRODS (Rule-Oriented Data management systems), to act as the data management system for the WTSI. iRODS provides a rule-based system management approach which makes data replication much easier and provides extra data protection. Unlike the metadata provided by traditional file systems, the metadata system of iRODS is comprehensive and allows users to customize their own application level metadata. Users and IT experts in the WTSI can then query the metadata to find and track data.</p> <p>The aim of this paper is to describe how we designed and used (from both system and user viewpoints) iRODS as a data management system. Details are given about the problems faced and the solutions found when iRODS was implemented. A simple use case describing how users within the WTSI use iRODS is also introduced.</p> <p>Conclusions</p> <p>iRODS has been implemented and works as the production system for the sequencing pipeline of the WTSI. Both biologists and IT experts can now track and manage data, which could not previously be achieved. This novel approach allows biologists to define their own metadata and query the genomic data using those metadata.</p

Microsurgical and tractographic anatomical study of insular and transsylvian transinsular approach

This study is to define the operative anatomy of the insula with emphasis on the transsylvian transinsular approach. The anatomy was studied in 15 brain specimens, among five were dissected by use of fiber dissection technique; diffusion tensor imaging of 10 healthy volunteers was obtained with a 1.5-T MR system. The temporal stem consists mainly of the uncinate fasciculus, inferior occipitofrontal fasciculus, Meyer’s loop of the optic radiation and anterior commissure. The transinsular approach requires an incision of the inferior limiting sulcus. In this procedure, the fibers of the temporal stem can be interrupted to various degrees. The fiber dissection technique is a very relevant and reliable method for neurosurgeons to study the details of brain anatomic features. The DTI fiber tracking technique can identify the fiber tracts of the temporal stem. Moreover, it will also help further functional study of human insula

Room temperature magnetic order on zigzag edges of narrow graphene nanoribbons

Magnetic order emerging in otherwise non-magnetic materials as carbon is a paradigmatic example of a novel type of s-p electron magnetism predicted to be of exceptional high-temperature stability. It has been demonstrated that atomic scale structural defects of graphene can host unpaired spins. However, it is still unclear under which conditions long-range magnetic order can emerge from such defect-bound magnetic moments. Here we propose that in contrast to random defect distributions, atomic scale engineering of graphene edges with specific crystallographic orientation, comprising edge atoms only from one sub-lattice of the bipartite graphene lattice, can give rise to a robust magnetic order. We employ a nanofabrication technique based on Scanning Tunneling Microscopy to define graphene nanoribbons with nanometer precision and well-defined crystallographic edge orientations. While armchair ribbons display quantum confinement gap, zigzag ribbons narrower than 7 nm reveal a bandgap of about 0.2 - 0.3 eV, which can be identified as a signature of interaction induced spin ordering along their edges. Moreover, a semiconductor to metal transition is revealed upon increasing the ribbon width, indicating the switching of the magnetic coupling between opposite ribbon edges from antiferromagnetic to ferromagnetic configuration. We found that the magnetic order on graphene edges of controlled zigzag orientation can be stable even at room temperature, raising hope for graphene-based spintronic devices operating under ambient conditions

Estimation of allele frequency and association mapping using next-generation sequencing data

<p>Abstract</p> <p>Background</p> <p>Estimation of allele frequency is of fundamental importance in population genetic analyses and in association mapping. In most studies using next-generation sequencing, a cost effective approach is to use medium or low-coverage data (e.g., < 15<it>X</it>). However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates.</p> <p>Results</p> <p>We evaluate a new maximum likelihood method for estimating allele frequencies in low and medium coverage next-generation sequencing data. The method is based on integrating over uncertainty in the data for each individual rather than first calling genotypes. This method can be applied to directly test for associations in case/control studies. We use simulations to compare the likelihood method to methods based on genotype calling, and show that the likelihood method outperforms the genotype calling methods in terms of: (1) accuracy of allele frequency estimation, (2) accuracy of the estimation of the distribution of allele frequencies across neutrally evolving sites, and (3) statistical power in association mapping studies. Using real re-sequencing data from 200 individuals obtained from an exon-capture experiment, we show that the patterns observed in the simulations are also found in real data.</p> <p>Conclusions</p> <p>Overall, our results suggest that association mapping and estimation of allele frequencies should not be based on genotype calling in low to medium coverage data. Furthermore, if genotype calling methods are used, it is usually better not to filter genotypes based on the call confidence score.</p