Spatially selective implementation of the adiabatic T2 prep sequence for magnetic resonance angiography of the coronary arteries.

In coronary magnetic resonance angiography, a magnetization-preparation scheme for T2 -weighting (T2 Prep) is widely used to enhance contrast between the coronary blood-pool and the myocardium. This prepulse is commonly applied without spatial selection to minimize flow sensitivity, but the nonselective implementation results in a reduced magnetization of the in-flowing blood and a related penalty in signal-to-noise ratio. It is hypothesized that a spatially selective T2 Prep would leave the magnetization of blood outside the T2 Prep volume unaffected and thereby lower the signal-to-noise ratio penalty. To test this hypothesis, a spatially selective T2 Prep was implemented where the user could freely adjust angulation and position of the T2 Prep slab to avoid covering the ventricular blood-pool and saturating the in-flowing spins. A time gap of 150 ms was further added between the T2 Prep and other prepulses to allow for in-flow of a larger volume of unsaturated spins. Consistent with numerical simulation, the spatially selective T2 Prep increased in vivo human coronary artery signal-to-noise ratio (42.3 ± 2.9 vs. 31.4 ± 2.2, n = 22, P < 0.0001) and contrast-to-noise-ratio (18.6 ± 1.5 vs. 13.9 ± 1.2, P = 0.009) as compared to those of the nonselective T2 Prep. Additionally, a segmental analysis demonstrated that the spatially selective T2 Prep was most beneficial in proximal and mid segments where the in-flowing blood volume was largest compared to the distal segments. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.

Development and evaluation of double locus sequence typing for molecular epidemiological investigations of Clostridium difficile.

Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are band-comparing methods often difficult to establish and which require reference strain collections. Here, we present the double locus sequence typing (DLST) scheme as a tool to analyse C. difficile isolates. Using a collection of clinical C. difficile isolates recovered during a 1-year period, we evaluated the performance of DLST and compared the results to multilocus sequence typing (MLST), a sequence-based method that has been used to study the structure of bacterial populations and highlight major clones. DLST had a higher discriminatory power compared to MLST (Simpson's index of diversity of 0.979 versus 0.965) and successfully identified all isolates of the study (100 % typeability). Previous studies showed that the discriminatory power of ribotyping was comparable to that of MLST; thus, DLST might be more discriminatory than ribotyping. DLST is easy to establish and provides several advantages, including absence of DNA extraction [polymerase chain reaction (PCR) is performed on colonies], no specific instrumentation, low cost and unambiguous definition of types. Moreover, the implementation of a DLST typing scheme on an Internet database, such as that previously done for Staphylococcus aureus and Pseudomonas aeruginosa ( http://www.dlst.org ), will allow users to easily obtain the DLST type by submitting directly sequencing files and will avoid problems associated with multiple databases.

Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

THE ASSOCIATION OF SEQUENCE OF HIRING PRACTICE AND BIOPHYSICAL COMPONENTS IN SCREENING PROBATIONARY FIREFIGHTERS

Variation in hiring procedures occurs within fire service human resource departments. In this study, City 1 and City 2 applicants were required to pass their biophysical assessments prior to being hired as firefighters at the beginning and end of the screening process, respectively. City 1 applicants demonstrated significantly lower resting heart rate (RHR), resting diastolic blood pressure (RDBP), body fat% (BF) and higher z-scores for BF, trunk flexibility (TF) and overall clinical assessment (p<0.05). Regression analysis found that age and conducting the biophysical assessment at the end of the screening process explained poorer biophysical assessment results in BF% (R2=21%), BF z-score (R2=22%), TF z-score (R2=10%) and overall clinical assessment z-score (R2=7%). Each of RHR (OR=1.06, CI=1.01-1.10), RDBP (OR=1.05, CI=1.00-1.11) and BF% (OR=1.20, CI=1.07-1.37) increased the odds of being a City 2 firefighter (p<0.05). Biophysical screening at the end of the hiring process may result in the hiring of a less healthy firefighter.

Complete Genome Sequence of Erwinia amylovora Bacteriophage

The complete genome of an Erwinia amylovora bacteriophage, vB_EamM_Ea35-70 (Ea35-70), is 271,084 bp, encodes 318 putative proteins, and contains one tRNA. Comparative analysis with other Myoviridae genomes suggests that Ea35-70 is related to the Phikzlikevirus genus within the family Myoviridae, since 26% of Ea35-70 proteins share homology to proteins in Pseudomonas phage φKZ.

AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis

Affiliation: Département de biochimie, Faculté de médecine, Université de Montréal

Foraminiferal and Pteropod Records in the Late Quaternary Sequence off Northern Kerala and Their Oceanographic and Climatic Significance

In the present investigation, an attempt is made to study late Quaternary foraminiferal and pteropod records of the shelf of northern Kerala and to evaluate their potentiality in paleocenographic and paleoclimatic reconstruction. The study gives details of sediment cores, general characteristics of foraminifera and pteropod species recorded from the examined samples and their systematic classification, spatial distribution of Recent foraminifera and pteropods and their response to varying bathymetry, nature of substrate, organic matter content in sediment and hydrography across the shelf. An attempt is also made to establish an integrated chronostratigraphy for the examined core sections. An effort is also made to identify microfaunal criteria useful in biostratigraphic division in shallow marine core sections. An attempt is made to infer various factors responsible for the change in microfaunal assemblage. Reconstruction of sea level changes during the last 36,000 years was attempted based on the pteropod record. The study reveals a bathymetric control on benthic/planktic (BF/PF) foraminiferal and pteropods/planktic foraminiferal (Pt/PF) abundance ratio. Bathymetric distribution pattern of BF/PF ratio is opposite to the (Pt/PF) ratio with decreasing trend of former from the shore across the shelf. Quantitative benthic foraminiferal record in the surficial sediments reveals a positive correlation between the diversity and bathymetry. R-mode cluster analysis performed on 30n significant Recent benthic foraminiferal, determines three major assemblage.

An Alternative Approach To Computer System Security Monitoring And Enhancement Through System Call Sequence Analysis

Modern computer systems are plagued with stability and security problems: applications lose data, web servers are hacked, and systems crash under heavy load. Many of these problems or anomalies arise from rare program behavior caused by attacks or errors. A substantial percentage of the web-based attacks are due to buffer overflows. Many methods have been devised to detect and prevent anomalous situations that arise from buffer overflows. The current state-of-art of anomaly detection systems is relatively primitive and mainly depend on static code checking to take care of buffer overflow attacks. For protection, Stack Guards and I-leap Guards are also used in wide varieties.This dissertation proposes an anomaly detection system, based on frequencies of system calls in the system call trace. System call traces represented as frequency sequences are profiled using sequence sets. A sequence set is identified by the starting sequence and frequencies of specific system calls. The deviations of the current input sequence from the corresponding normal profile in the frequency pattern of system calls is computed and expressed as an anomaly score. A simple Bayesian model is used for an accurate detection.Experimental results are reported which show that frequency of system calls represented using sequence sets, captures the normal behavior of programs under normal conditions of usage. This captured behavior allows the system to detect anomalies with a low rate of false positives. Data are presented which show that Bayesian Network on frequency variations responds effectively to induced buffer overflows. It can also help administrators to detect deviations in program flow introduced due to errors.

Studies on underwater propagation development of programmable arrays

The thesis presented here includes the designing of underwater transducer arrays, taking into account the ‘interaction effects’ [30] among the closely packed radiators. Methods of minimizing the ‘interaction effects‘ by modifying the radiating aperture, are investigated. The need for this study arises as it is one of the important peculiar limitations that stands in the way of achieving maximum range of transmission of acoustic signals. Application of the modified array format for the generation of narrow beam low frequency sound waves, through nonlinear interactions, is discussed. Other techniques that can be advantageously exploited in array synthesis are also investigated

Anomaly Detection Using System Call Sequence Sets.

This paper discusses our research in developing a generalized and systematic method for anomaly detection. The key ideas are to represent normal program behaviour using system call frequencies and to incorporate probabilistic techniques for classification to detect anomalies and intrusions. Using experiments on the sendmail system call data, we demonstrate that concise and accurate classifiers can be constructed to detect anomalies. An overview of the approach that we have implemented is provided.

RNS based programmable multi-mode decimation filter for WCDMA and WiMAX

The recent trends envisage multi-standard architectures as a promising solution for the future wireless transceivers to attain higher system capacities and data rates. The computationally intensive decimation filter plays an important role in channel selection for multi-mode systems. An efficient reconfigurable implementation is a key to achieve low power consumption. To this end, this paper presents a dual-mode Residue Number System (RNS) based decimation filter which can be programmed for WCDMA and 802.16e standards. Decimation is done using multistage, multirate finite impulse response (FIR) filters. These FIR filters implemented in RNS domain offers high speed because of its carry free operation on smaller residues in parallel channels. Also, the FIR filters exhibit programmability to a selected standard by reconfiguring the hardware architecture. The total area is increased only by 24% to include WiMAX compared to a single mode WCDMA transceiver. In each mode, the unused parts of the overall architecture is powered down and bypassed to attain power saving. The performance of the proposed decimation filter in terms of critical path delay and area are tabulated.

Dual-mode RNS based programmable decimation filter for WCDMA and WLANa

The recent trends envisage multi-standard architectures as a promising solution for the future wireless transceivers. The computationally intensive decimation filter plays an important role in channel selection for multi-mode systems. An efficient reconfigurable implementation is a key to achieve low power consumption. To this end, this paper presents a dual-mode Residue Number System (RNS) based decimation filter which can be programmed for WCDMA and 802.11a standards. Decimation is done using multistage, multirate finite impulse response (FIR) filters. These FIR filters implemented in RNS domain offers high speed because of its carry free operation on smaller residues in parallel channels. Also, the FIR filters exhibit programmability to a selected standard by reconfiguring the hardware architecture. The total area is increased only by 33% to include WLANa compared to a single mode WCDMA transceiver. In each mode, the unused parts of the overall architecture is powered down and bypassed to attain power saving. The performance of the proposed decimation filter in terms of critical path delay and area are tabulated

Code clones in program test sequence identification

Code clones are portions of source code which are similar to the original program code. The presence of code clones is considered as a bad feature of software as the maintenance of software becomes difficult due to the presence of code clones. Methods for code clone detection have gained immense significance in the last few years as they play a significant role in engineering applications such as analysis of program code, program understanding, plagiarism detection, error detection, code compaction and many more similar tasks. Despite of all these facts, several features of code clones if properly utilized can make software development process easier. In this work, we have pointed out such a feature of code clones which highlight the relevance of code clones in test sequence identification. Here program slicing is used in code clone detection. In addition, a classification of code clones is presented and the benefit of using program slicing in code clone detection is also mentioned in this work.

DNA Sequence Representation methods

DNA sequence representation methods are used to denote a gene structure effectively and help in similarities/dissimilarities analysis of coding sequences. Many different kinds of representations have been proposed in the literature. They can be broadly classified into Numerical, Graphical, Geometrical and Hybrid representation methods. DNA structure and function analysis are made easy with graphical and geometrical representation methods since it gives visual representation of a DNA structure. In numerical method, numerical values are assigned to a sequence and digital signal processing methods are used to analyze the sequence. Hybrid approaches are also reported in the literature to analyze DNA sequences. This paper reviews the latest developments in DNA Sequence representation methods. We also present a taxonomy of various methods. A comparison of these methods where ever possible is also done