Adhesion capability to fish mucus, which can be affected by environmental conditions, is considered to be a key virulence factor of Vibrio alginolyticus although the molecular mechanism is still unclear. In the present study, V. alginolyticus was treated with stress conditions including Cu2+ (50 mg/L), Pb2+ (100 mg/L), Hg2+ (50 mg/L) and low pH (pH 5). We found these stress treatments were capable of reducing the adhesion of V. alginolyticus, while the expression levels of multiple genes were significantly changed according to the results of high throughput sequencing. The expression of randomly selected genes was confirmed by QPCR, which reinforced the reliability of the sequencing data. Ontology assignments and KEGG pathway analysis indicated that stress treatments affect pathways that may be related to adhesion. Our results identified genes which might play a key role in the adhesion process of V. alginolyticus, which could lay a foundation for further functional analysis of these genes in the process of adhesion. As these genes were sensitive to environmental factors, this may explain why the adhesion process can be influenced by environmental factors.Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-015-0411-9) contains supplementary material, which is available to authorized users.

Adhesion is a critical step in the initial stage of Vibrio alginolyticus infection; therefore, it is important to understand the underlying mechanisms governing the adhesion of V. alginolyticus and determine if environmental factors have any effect. A greater understanding of this process may assist in developing preventive measures for reducing infection. In our previous research, we presented the first RNA-seq data from V. alginolyticus cultured under stress conditions that resulted in reduced adhesion. Based on the RNA-seq data, we found that the Tricarboxylic acid cycle (TCA pathway) might be closely related to adhesion. Environmental interactions with the TCA pathway might alter adhesion. To validate this, bioinformatics analysis, quantitative Real-Time PCR (qPCR), RNAi, and in vitro adhesion assays were performed, while V. alginolyticus was treated with various stresses including temperature, pH, salinity, and starvation. The expression of genes involved in the TCA pathway was confirmed by qPCR, which reinforced the reliability of the sequencing data. Silencing of these genes was capable of reducing the adhesion ability of V. alginolyticus. Adhesion of V. alginolyticus is influenced substantially by environmental factors and the TCA pathway is sensitive to some environmental stresses, especially changes in pH and starvation. Our results indicated that (1) the TCA pathway plays a key role in V. alginolyticus adhesion: (2) the TCA pathway is sensitive to environmental stresses.

Adhesion is an important virulence factor of Vibrio alginolyticus. This factor may be affected by environmental conditions; however, its molecular mechanism remains unclear. In our previous research, adhesion deficient strains were obtained by culturing V. alginolyticus under stresses including Cu, Pb, Hg, and low pH. With RNA-seq and bioinformatics analysis, we found that all of these stress treatments significantly affected the flagellar assembly pathway, which may play an important role in V. alginolyticus adhesion. Therefore, we hypothesized that the environmental stresses of the flagellar assembly pathway may be one way in which environmental conditions affect adhesion. To verify our hypothesis, a bioinformatics analysis, QPCR, RNAi, in vitro adhesion assay and motility assay were performed. Our results indicated that (1) the flagellar assembly pathway was sensitive to environmental stresses, (2) the flagellar assembly pathway played an important role in V. alginolyticus adhesion, and (3) motility is not the only way in which the flagellar assembly pathway affects adhesion.

Conventional stereotactic surgery has evolved from a ring-based system with a simple software which calculated few parameters to frameless intraoperative localization systems that provide the surgeon with, real-time localization and correlation with several imaging modalities. The localization system described in this paper is an opto-electronic system that uses infrared emitters and three precalibrated CCD cameras. The system was chosen among others for the following reasons: it tracks target points defined by up to 256 miniature light emitting diodes, and its accuracy in locating the spatial positron of a diode marker in the operating volume 1.0 × 1.0 m at a distance of 2.0 m is 0.1 mm with a resolution better than 0.01 mm. Systems like this one can track and define the position and orientation of any object in the field view of the camera. This is done by attaching a few small infrared emitters (light emitting diodes) to the surface of each ''rigid body'' (surgical instrument) being tracked. Subsequently, through a calibration process a corresponding rigid body file is created. This rigid body file represents this particular object (i.e. surgical tool, microscope) and defines a local coordinate system that identifies each translation and orientation of that tool with respect to the camera coordinate system. This in turn is transferred into the computed tomo-graphic/magnetic resonance imaging coordinate system by a process referred to as coordinate matching. Fiducial markers are placed on the patient''s head prior to image scanning. Coordinate matching involves establishing the transformation matrix between the computed tomographic/magnetic resonance imaging coordinate system and the camera coordinate system using the fiducial markers as common points in both coordinate systems. This process is done during the initial calibration process. The system is integrated to a two-dimensional and three-dimensional multi-imaging neurosurgical software program (Neurosurgical Planning System, Detroit, Mich., 48201). By feeding in real-time the numerical data which represent the position and orientation of the surgical tool to the neurosurgical software, a cursor is displayed on the computer monitor indicating the position of the surgical tool with respect to the physical anatomy of the brain in several projections. In addition to the unique advantage of being able to track any surgical tool in real-time along with surgical preplanning and simulation, this system provides a complete frameless stereotaxis system that could be applied to the same extent as a frame-based system.

This paper describes our attempt at NomBank-based automatic Semantic Role Labeling (SRL). NomBank is a project at New York University to annotate the argument structures for common nouns in the Penn Treebank II corpus. We treat the NomBank SRL task as a classification problem and explore the possibility of adapting features previously shown useful in PropBank-based SRL systems. Various NomBank-specific features are explored. On test section 23, our best system achieves F1 score of 72.73 (69.14) when correct (automatic) syntactic parse trees are used. To our knowledge, this is the first reported automatic NomBank SRL system.