scholarly journals Genomic Features of Rickettsia heilongjiangensis Revealed by Intraspecies Comparison and Detailed Comparison With Rickettsia japonica

2019 ◽  
Vol 10 ◽  
Author(s):  
Kentaro Kasama ◽  
Hiromi Fujita ◽  
Seigo Yamamoto ◽  
Tadasuke Ooka ◽  
Yasuhiro Gotoh ◽  
...  
Keyword(s):  
Detailed Comparison ◽  
Genomic Features ◽  
Rickettsia Heilongjiangensis

scholarly journals The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Ruriko Nishida ◽  
Keiji Nakamura ◽  
Itsuki Taniguchi ◽  
Kazunori Murase ◽  
Tadasuke Ooka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Common Ancestor ◽  
Detailed Comparison ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Genomic Features ◽  
Content Type ◽  
Complete Genomes ◽  
The Common

Shiga toxin (Stx)-producing Escherichia coli (STEC) are foodborne pathogens causing serious diseases, such as haemorrhagic colitis and haemolytic uraemic syndrome. Although O157:H7 STEC strains have been the most prevalent, incidences of STEC infections by several other serotypes have recently increased. O121:H19 STEC is one of these major non-O157 STECs, but systematic whole genome sequence (WGS) analyses have not yet been conducted on this STEC. Here, we performed a global WGS analysis of 638 O121:H19 strains, including 143 sequenced in this study, and a detailed comparison of 11 complete genomes, including four obtained in this study. By serotype-wide WGS analysis, we found that O121:H19 strains were divided into four lineages, including major and second major lineages (named L1 and L3, respectively), and that the locus of enterocyte effacement (LEE) encoding a type III secretion system (T3SS) was acquired by the common ancestor of O121:H19. Analyses of 11 complete genomes belonging to L1 or L3 revealed remarkable interlineage differences in the prophage pool and prophage-encoded T3SS effector repertoire, independent acquisition of virulence plasmids by the two lineages, and high conservation in the prophage repertoire, including that for Stx2a phages in lineage L1. Further sequence determination of complete Stx2a phage genomes of 49 strains confirmed that Stx2a phages in lineage L1 are highly conserved short-tailed phages, while those in lineage L3 are long-tailed lambda-like phages with notable genomic diversity, suggesting that an Stx2a phage was acquired by the common ancestor of L1 and has been stably maintained. Consistent with these genomic features of Stx2a phages, most lineage L1 strains produced much higher levels of Stx2a than lineage L3 strains. Altogether, this study provides a global phylogenetic overview of O121:H19 STEC and shows the interlineage genomic differences and the highly conserved genomic features of the major lineage within this serotype of STEC.

Light front field theory: An advanced Primer

2007 ◽  
Vol 57 (3) ◽  
Author(s):  
L'ubomír Martinovič
Keyword(s):  
Field Theory ◽  
Detailed Comparison ◽  
Light Front ◽  
Two Dimensional ◽  
Schwinger Model ◽  
Initial Space ◽  
Model Hamiltonian ◽  
Spatial Volume ◽  
Hamiltonian Perturbation Theory ◽  
Light Front Quantization

Light front field theory: An advanced PrimerWe present an elementary introduction to quantum field theory formulated in terms of Dirac's light front variables. In addition to general principles and methods, a few more specific topics and approaches based on the author's work will be discussed. Most of the discussion deals with massive two-dimensional models formulated in a finite spatial volume starting with a detailed comparison between quantization of massive free fields in the usual field theory and the light front (LF) quantization. We discuss basic properties such as relativistic invariance and causality. After the LF treatment of the soluble Federbush model, a LF approach to spontaneous symmetry breaking is explained and a simple gauge theory - the massive Schwinger model in various gauges is studied. A LF version of bosonization and the massive Thirring model are also discussed. A special chapter is devoted to the method of discretized light cone quantization and its application to calculations of the properties of quantum solitons. The problem of LF zero modes is illustrated with the example of the two-dimensional Yukawa model. Hamiltonian perturbation theory in the LF formulation is derived and applied to a few simple processes to demonstrate its advantages. As a byproduct, it is shown that the LF theory cannot be obtained as a "light-like" limit of the usual field theory quantized on an initial space-like surface. A simple LF formulation of the Higgs mechanism is then given. Since our intention was to provide a treatment of the light front quantization accessible to postgradual students, an effort was made to discuss most of the topics pedagogically and a number of technical details and derivations are contained in the appendices.

Gaunilo Parodies Anselm

2014 ◽  
Vol 17 (1) ◽  
pp. 45-71
Author(s):  
Geo Siegwart
Keyword(s):  
Detailed Comparison ◽  
The Third ◽  
Common Structure ◽  
Logical Reconstruction ◽  
Points Of View ◽  
And Function

The main objective is an interpretation of the island parody, in particular a logical reconstruction of the parodying argument that stays close to the text. The parodied reasoning is identified as the proof in the second chapter of the Proslogion, more specifically, this proof as it is represented by Gaunilo in the first chapter of his Liber pro insipiente. The second task is a detailed comparison between parodied and parodying argument as well as an account of their common structure. The third objective is a tentative characterization of the nature and function of parodies of arguments. It seems that parodying does not add new pertinent points of view to the usual criticism of an argument.

Genome sequence of Novosphingobium malaysiense strain MUSC 273T, novel alpha-proteobacterium isolated from intertidal soil

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
Nurul-Syakima Ab Mutalib ◽  
Learn-Han Lee
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolite ◽  
Genome Sequence ◽  
Catalase Activity ◽  
Gene Clusters ◽  
Rrna Genes ◽  
Gram Negative ◽  
Genomic Features

Novosphingobium malaysiense strain MUSC 273T is a recently identified Gram-negative, aerobic alpha-proteobacterium. The strain was isolated from intertidal soil with strong catalase activity. The genome sequence comprises 5,027,021 bp, with 50 tRNA and 3 rRNA genes. Further analysis identified presence of secondary metabolite gene clusters within genome of MUSC 273T. Knowledge of the genomic features of the strain may allow further biotechnological exploitation, particularly for production of secondary metabolites as well as production of industrially important enzymes

Sequence-Based Deep Learning Frameworks on Enhancer-Promoter Interactions Prediction

2020 ◽  
Vol 26 ◽  
Author(s):  
Xiaoping Min ◽  
Fengqing Lu ◽  
Chunyan Li
Keyword(s):  
Gene Expression ◽  
Deep Learning ◽  
Dna Sequences ◽  
Experimental Methods ◽  
Learning Methods ◽  
Comprehensive Review ◽  
Genomic Features ◽  
Disease Mechanisms ◽  
Evaluation Strategies ◽  
Learning Frameworks

: Enhancer-promoter interactions (EPIs) in the human genome are of great significance to transcriptional regulation which tightly controls gene expression. Identification of EPIs can help us better deciphering gene regulation and understanding disease mechanisms. However, experimental methods to identify EPIs are constrained by the fund, time and manpower while computational methods using DNA sequences and genomic features are viable alternatives. Deep learning methods have shown promising prospects in classification and efforts that have been utilized to identify EPIs. In this survey, we specifically focus on sequence-based deep learning methods and conduct a comprehensive review of the literatures of them. We first briefly introduce existing sequence-based frameworks on EPIs prediction and their technique details. After that, we elaborate on the dataset, pre-processing means and evaluation strategies. Finally, we discuss the challenges these methods are confronted with and suggest several future opportunities.

The East-Syriac Reception of Evagrius’s Gnostic Chapters

2017 ◽  
Author(s):  
Jason Scully
Keyword(s):  
Detailed Comparison ◽  
Fifth Century ◽  
Sixth Century ◽  
Human Soul ◽  
The Future

The first chapter demonstrates that even though Isaac quotes Evagrius throughout much of his writing, Isaac does not adopt Evagrius’s eschatological framework. In order to reach this conclusion, this chapter conducts a detailed comparison of two Syriac translations of the Gnostic Chapters, which is the Evagrian text that Isaac quotes most often. While the sixth-century Syriac version of the Gnostic Chapters includes a detailed eschatological consideration of the human soul in the future world, the fifth-century Syriac version is void of any distinctive eschatological framework. Since Isaac only used the fifth-century Syriac version of the Gnostic Chapters, he cannot have derived his eschatological framework from Evagrius. Rather, following Babai the Great, who established a framework for interpreting the fifth-century Syriac version of the Gnostic Chapters, Isaac interprets Evagrius’s Gnostic Chapters as a work describing the journey of asceticism.

QCD at Fixed Order: Processes

2018 ◽  
Author(s):  
John Campbell ◽  
Joey Huston ◽  
Frank Krauss
Keyword(s):  
Hadron Collider ◽  
Detailed Comparison ◽  
Theoretical Description ◽  
Higgs Bosons ◽  
Final States ◽  
Collider Physics ◽  
Wide Range ◽  
Theoretical Predictions ◽  
Fixed Order ◽  
The Subject

At the core of any theoretical description of hadron collider physics is a fixed-order perturbative treatment of a hard scattering process. This chapter is devoted to a survey of fixed-order predictions for a wide range of Standard Model processes. These range from high cross-section processes such as jet production to much more elusive reactions, such as the production of Higgs bosons. Process by process, these sections illustrate how the techniques developed in Chapter 3 are applied to more complex final states and provide a summary of the fixed-order state-of-the-art. In each case, key theoretical predictions and ideas are identified that will be the subject of a detailed comparison with data in Chapters 8 and 9.

scholarly journals Compressive behaviours of octet-truss lattices

2020 ◽  
Vol 234 (16) ◽  
pp. 3257-3269 ◽  
Author(s):  
Yifan Li ◽  
Huaiyuan Gu ◽  
Martyn Pavier ◽  
Harry Coules
Keyword(s):  
Failure Modes ◽  
Density Ratio ◽  
Three Dimensional ◽  
Compressive Load ◽  
High Strength ◽  
Detailed Comparison ◽  
Compressive Response ◽  
Beam Elements ◽  
Structural Applications ◽  
Octet Truss

Octet-truss lattice structures can be used for lightweight structural applications due to their high strength-to-density ratio. In this research, octet-truss lattice specimens were fabricated by stereolithography additive manufacturing with a photopolymer resin. The mechanical properties of this structure have been examined in three orthogonal orientations under the compressive load. Detailed comparison and description were carried out on deformation mechanisms and failure modes in different lattice orientations. Finite element models using both beam elements and three-dimensional solid elements were used to simulate the compressive response of this structure. Both the load reaction and collapse modes obtained in simulations were compared with test results. Our results indicate that three-dimensional continuum element models are required to accurately capture the behaviour of real trusses, taking into account the effects of finite-sized beams and joints.

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