Accurate Localization of the Integration Sites of Two Genomic Islands at Single-Nucleotide Resolution in the Genome of Bacillus cereus ATCC 10987

We have identified two genomic islands, that is, BCEGI-1 and BCEGI-2, in the genome of Bacillus cereus ATCC 10987, based on comparative analysis with Bacillus cereus ATCC 14579. Furthermore, by using the cumulative GC profile and performing homology searches between the two genomes, the integration sites of the two genomic islands were determined at single-nucleotide resolution. BCEGI-1 is integrated between 159705 bp and 198000 bp, whereas BCEGI-2 is integrated between the end of ORF BCE4594 and the start of the intergenic sequence immediately following BCE4626, that is, from 4256803 bp to 4285534 bp. BCEGI-1 harbors two bacterial Tn7 transposons, which have two sets of genes encoding TnsA, B, C, and D. It is generally believed that unlike the TnsABC+E pathway, the TnsABC+D pathway would only promote vertical transmission to daughter cells. The evidence presented in this paper, however, suggests a role of the TnsABC+D pathway in the horizontal transfer of some genomic islands

GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences

In order to understand the evolution, structure and function of genomes, it is important to know the general compositional features of DNA sequences. Based on the quadratic divergence, a new segmentation algorithm to partition a given genome or DNA sequence into compositionally distinct domains has been put forward. With the aid of the technique of cumulative GC profile, the distribution of segmentation points can be displayed intuitively. We have therefore developed them into GC-Profile, an interactive web-based software system, which can be used to segment prokaryotic and eukaryotic genomes. GC-Profile provides a quantitative and qualitative view of genome organization. Based on the obtained results, the relationships between the G+C content and other genomic features, such as distributions of genes and CpG islands, can be analyzed in a perceivable manner. It shows that GC-Profile would be an appropriate starting point for analyzing the isochore structure of higher eukaryotic genomes, and an intuitive tool for identifying genomic islands in prokaryotic genomes. GC-Profile is freely available at the website . In addition, precompiled binaries, together with examples and documentation, can also be freely downloaded for a local execution

Progressive amorphization of GeSbTe phase-change material under electron beam irradiation

Fast and reversible phase transitions in chalcogenide phase-change materials (PCMs), in particular, Ge-Sb-Te compounds, are not only of fundamental interests, but also make PCMs based random access memory (PRAM) a leading candidate for non-volatile memory and neuromorphic computing devices. To RESET the memory cell, crystalline Ge-Sb-Te has to undergo phase transitions firstly to a liquid state and then to an amorphous state, corresponding to an abrupt change in electrical resistance. In this work, we demonstrate a progressive amorphization process in GeSb2Te4 thin films under electron beam irradiation on transmission electron microscope (TEM). Melting is shown to be completely absent by the in situ TEM experiments. The progressive amorphization process resembles closely the cumulative crystallization process that accompanies a continuous change in electrical resistance. Our work suggests that if displacement forces can be implemented properly, it should be possible to emulate symmetric neuronal dynamics by using PCMs

ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes

BACKGROUND: It necessary to use highly accurate and statistics-based systems for viral and phage genome annotations. The GeneMark systems for gene-finding in virus and phage genomes suffer from some basic drawbacks. This paper puts forward an alternative approach for viral and phage gene-finding to improve the quality of annotations, particularly for newly sequenced genomes. RESULTS: The new system ZCURVE_V has been run for 979 viral and 212 phage genomes, respectively, and satisfactory results are obtained. To have a fair comparison with the currently available software of similar function, GeneMark, a total of 30 viral genomes that have not been annotated by GeneMark are selected to be tested. Consequently, the average specificity of both systems is well matched, however the average sensitivity of ZCURVE_V for smaller viral genomes (< 100 kb), which constitute the main parts of viral genomes sequenced so far, is higher than that of GeneMark. Additionally, for the genome of Amsacta moorei entomopoxvirus, probably with the lowest genomic GC content among the sequenced organisms, the accuracy of ZCURVE_V is much better than that of GeneMark, because the later predicts hundreds of false-positive genes. ZCURVE_V is also used to analyze well-studied genomes, such as HIV-1, HBV and SARS-CoV. Accordingly, the performance of ZCURVE_V is generally better than that of GeneMark. Finally, ZCURVE_V may be downloaded and run locally, particularly facilitating its utilization, whereas GeneMark is not downloadable. Based on the above comparison, it is suggested that ZCURVE_V may serve as a preferred gene-finding tool for viral and phage genomes newly sequenced. However, it is also shown that the joint application of both systems, ZCURVE_V and GeneMark, leads to better gene-finding results. The system ZCURVE_V is freely available at: . CONCLUSION: ZCURVE_V may serve as a preferred gene-finding tool used for viral and phage genomes, especially for anonymous viral and phage genomes newly sequenced

Accurate localization of the integration sites of two genomic islands at single-nucleotide resolution in the genome of Bacillus cereus ATCC 10987

We have identified two genomic islands, that is, BCEGI-1 and BCEGI-2, in the genome of Bacillus cereus ATCC 10987, based on comparative analysis with Bacillus cereus ATCC 14579. Furthermore, by using the cumulative GC profile and performing homology searches between the two genomes, the integration sites of the two genomic islands were determined at single-nucleotide resolution. BCEGI-1 is integrated between 159705 bp and 198000 bp, whereas BCEGI-2 is integrated between the end of ORF BCE4594 and the start of the intergenic sequence immediately following BCE4626, that is, from 4256803 bp to 4285534 bp. BCEGI-1 harbors two bacterial Tn7 transposons, which have two sets of genes encoding TnsA, B, C, and D. It is generally believed that unlike the TnsABC+E pathway, the TnsABC+D pathway would only promote vertical transmission to daughter cells. The evidence presented in this paper, however, suggests a role of the TnsABC+D pathway in the horizontal transfer of some genomic islands

Regularization of the Shock Wave Solution to the Riemann Problem for the Relativistic Burgers Equation

The regularization of the shock wave solution to the Riemann problem for the relativistic Burgers equation is considered. For Riemann initial data consisting of a single decreasing jump, we find that the regularization of nonlinear convective term cannot capture the correct shock wave solution. In order to overcome it, we consider a new regularization technique called the observable divergence method introduced by Mohseni and discover that it can capture the correct shock wave solution. In addition, we take the Helmholtz filter for the fully explicit computation

THERMAL OSCILLATION ARISING IN A HEAT SHOCK OF A POROUS HIERARCHY AND ITS APPLICATION

A building or a bridge might collapse after a heat shock. This paper shows that a porous hierarchy of a coating can effectively prevent a building or a bridge from such damage. A cocoon’s geometrical structure is studied and its resistance to the heat shock is revealed by a thermal oscillator. The theoretical model reveals an extremely low frequency of the thermal oscillator, which is very important for cocoons’ biomechanism, especially in the heat insulation function. At the same time, it shows that the cocoons have the best thickness to protect the pupa from the environment. In addition, surface temperature measurement of hierarchical mulberry leaves is performed. This work provides new insights into biomimetic design of the protective building and coatings

Long-term unmet needs after stroke:systematic review of evidence from survey studies

OBJECTIVES: To synthesise evidence on longer term unmet needs perceived by stroke survivors, and psychometric properties of the tools used to evaluate unmet care needs after stroke. DESIGN: Systematic review. SETTING: Community or patients' home. PARTICIPANTS: Stroke survivors. METHODS: We searched PubMed, PsycINFO, CINAHL, EMBASE from inception to 31 March 2018 to identify survey studies that evaluated unmet needs perceived by stroke survivors after hospital discharge. Reported unmet needs were categorised under three domains: body functioning, activity/participation and environmental factors. Ranges of prevalence rates of unmet needs reported in studies were presented. RESULTS: We included 19 eligible studies, with considerable heterogeneity in patients, survey methods and results. Psychometric properties of two stroke-specific tools were formally evaluated, indicating their moderate reliability and content/concurrent validity. The median number of reported unmet needs per stroke survivor was from two to five, and the proportion of stroke survivors with at least one unmet needs was on average 73.8% (range 19.8%- 91.7%). Unmet needs perceived by stroke survivors included 55 records of unmet body functioning needs, 47 records of unmet activities/participatory needs and 101 records of unmet environmental needs. Common unmet service needs were unmet information needs (3.1%- 65.0%), transport (5.4%-53.0%), home help/personal care (4.7%-39.3%) and therapy (2.0%-35.7%). CONCLUSIONS: The prevalence of unmet long-term needs is high among stroke survivors, and there is considerable heterogeneity in type and frequency of specific unmet needs. More research is required to link regular assessment of long-term unmet needs of stroke survivors with the provision of cost-effective patient-centred health and social care services

Polylogarithmic Approximation Algorithm for k-Connected Directed Steiner Tree on Quasi-Bipartite Graphs

In the k-Connected Directed Steiner Tree problem (k-DST), we are given a directed graph G = (V,E) with edge (or vertex) costs, a root vertex r, a set of q terminals T, and a connectivity requirement k > 0; the goal is to find a minimum-cost subgraph H of G such that H has k edge-disjoint paths from the root r to each terminal in T. The k-DST problem is a natural generalization of the classical Directed Steiner Tree problem (DST) in the fault-tolerant setting in which the solution subgraph is required to have an r,t-path, for every terminal t, even after removing k-1 vertices or edges. Despite being a classical problem, there are not many positive results on the problem, especially for the case k ? 3. In this paper, we present an O(log k log q)-approximation algorithm for k-DST when an input graph is quasi-bipartite, i.e., when there is no edge joining two non-terminal vertices. To the best of our knowledge, our algorithm is the only known non-trivial approximation algorithm for k-DST, for k ? 3, that runs in polynomial-time Our algorithm is tight for every constant k, due to the hardness result inherited from the Set Cover problem