Abstract: Network on a chip (NoC) has been proposed as a viable solution to counter the inefficiency of buses in the current VLSI on-chip interconnects. However, as the silicon chip accommodates more transistors, the probability of transient faults is increasing, making fault tolerance a key concern in scaling chips. In packet based communication on a chip, transient failures can corrupt the data packet and hence, undermine the accuracy of data communication. In this paper, we present a comparative analysis of transient fault tolerant techniques including end-to-end, node-by-node, and stochastic communication based on flooding principle.
Abstract: Pattern recognition is the research area of Artificial
Intelligence that studies the operation and design of systems that
recognize patterns in the data. Important application areas are image
analysis, character recognition, fingerprint classification, speech
analysis, DNA sequence identification, man and machine
diagnostics, person identification and industrial inspection. The
interest in improving the classification systems of data analysis is
independent from the context of applications. In fact, in many
studies it is often the case to have to recognize and to distinguish
groups of various objects, which requires the need for valid
instruments capable to perform this task. The objective of this article
is to show several methodologies of Artificial Intelligence for data
classification applied to biomedical patterns. In particular, this work
deals with the realization of a Computer-Aided Detection system
(CADe) that is able to assist the radiologist in identifying types of
mammary tumor lesions. As an additional biomedical application of
the classification systems, we present a study conducted on blood
samples which shows how these methods may help to distinguish
between carriers of Thalassemia (or Mediterranean Anaemia) and
healthy subjects.
Abstract: In this study, we illustrated the performance and
microbial community of single- and two-phase systems anaerobically
co-digesting cassava pulp and pig manure. The results showed that
the volatile solid reduction and biogas productivity of two-phase
CSTR were 66 ± 4% and 2000 ± 210 ml l-1 d-1, while those of singlephase
CSTR were 59 ± 1% and 1670 ± 60 ml l-1 d-1, respectively. Codigestion
in two-phase CSTR gave higher 12% solid degradation and
25% methane production than single-phase CSTR. Phylogenetic
analysis of 16S rDNA clone library revealed that the Bacteroidetes
were the most abundant group, followed by the Clostridia in singlephase
CSTR. In hydrolysis/acidification reactor of two-phase system,
the bacteria within the phylum Firmicutes, especially Clostridium,
Eubacteriaceae and Lactobacillus were the dominant phylogenetic
groups. Among the Archaea, Methanosaeta sp. was the exclusive
predominant in both digesters while the relative abundance of
Methanosaeta sp. and Methanospirillum hungatei differed between
the two systems.
Abstract: Oxidative stress is considered to be the cause for onset
and the progression of type 2 diabetes mellitus (T2DM) and
complications including neuropathy. It is a deleterious process that
can be an important mediator of damage to cell structures: protein,
lipids and DNA. Data suggest that in patients with diabetes and
diabetic neuropathy DNA repair is impaired, which prevents effective
removal of lesions. Objective: The aim of our study was to evaluate
the association of the hOGG1 (326 Ser/Cys) and XRCC1 (194
Arg/Trp, 399 Arg/Gln) gene polymorphisms whose protein is
involved in the BER pathway with DNA repair efficiency in patients
with diabetes type 2 and diabetic neuropathy compared to the healthy
subjects. Genotypes were determined by PCR-RFLP analysis in 385
subjects, including 117 with type 2 diabetes, 56 with diabetic
neuropathy and 212 with normal glucose metabolism. The
polymorphisms studied include codon 326 of hOGG1 and 194, 399
of XRCC1 in the base excision repair (BER) genes. Comet assay was
carried out using peripheral blood lymphocytes from the patients and
controls. This test enabled the evaluation of DNA damage in cells
exposed to hydrogen peroxide alone and in the combination with the
endonuclease III (Nth). The results of the analysis of polymorphism
were statistically examination by calculating the odds ratio (OR) and
their 95% confidence intervals (95% CI) using the ¤ç2-tests. Our data
indicate that patients with diabetes mellitus type 2 (including those
with neuropathy) had higher frequencies of the XRCC1 399Arg/Gln
polymorphism in homozygote (GG) (OR: 1.85 [95% CI: 1.07-3.22],
P=0.3) and also increased frequency of 399Gln (G) allele (OR: 1.38
[95% CI: 1.03-1.83], P=0.3). No relation to other polymorphisms
with increased risk of diabetes or diabetic neuropathy. In T2DM
patients complicated by neuropathy, there was less efficient repair of
oxidative DNA damage induced by hydrogen peroxide in both the
presence and absence of the Nth enzyme. The results of our study
suggest that the XRCC1 399 Arg/Gln polymorphism is a significant
risk factor of T2DM in Polish population. Obtained data suggest a
decreased efficiency of DNA repair in cells from patients with
diabetes and neuropathy may be associated with oxidative stress.
Additionally, patients with neuropathy are characterized by even
greater sensitivity to oxidative damage than patients with diabetes,
which suggests participation of free radicals in the pathogenesis of
neuropathy.
Abstract: Yeast cells live in a constantly changing environment that requires the continuous adaptation of their genomic program in order to sustain their homeostasis, survive and proliferate. Due to the advancement of high throughput technologies, there is currently a large amount of data such as gene expression, gene deletion and protein-protein interactions for S. Cerevisiae under various environmental conditions. Mining these datasets requires efficient computational methods capable of integrating different types of data, identifying inter-relations between different components and inferring functional groups or 'modules' that shape intracellular processes. This study uses computational methods to delineate some of the mechanisms used by yeast cells to respond to environmental changes. The GRAM algorithm is first used to integrate gene expression data and ChIP-chip data in order to find modules of coexpressed and co-regulated genes as well as the transcription factors (TFs) that regulate these modules. Since transcription factors are themselves transcriptionally regulated, a three-layer regulatory cascade consisting of the TF-regulators, the TFs and the regulated modules is subsequently considered. This three-layer cascade is then modeled quantitatively using artificial neural networks (ANNs) where the input layer corresponds to the expression of the up-stream transcription factors (TF-regulators) and the output layer corresponds to the expression of genes within each module. This work shows that (a) the expression of at least 33 genes over time and for different stress conditions is well predicted by the expression of the top layer transcription factors, including cases in which the effect of up-stream regulators is shifted in time and (b) identifies at least 6 novel regulatory interactions that were not previously associated with stress-induced changes in gene expression. These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully model biological pathways and capture quantitative dependencies between distant regulators and downstream genes.
Abstract: The main aim is to perform mutational analysis of CTLA4 gene Exon 1 in SLE patients. A total of 61 SLE patients fulfilling “American College of Rheumatology (ACR) criteria" and 61 controls were enrolled in this study. The region of CTLA4 gene exon 1 was amplified by using Step-down PCR technique. Extracted DNA of band 354 bp was sequenced to analyze mutations in the exon-1 of CTLA-4 gene. Further, protein sequences were identified from nucleotide sequences of CTLA4 Exon 1 by using Expasy software and through Blast P software it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. No variations were found after patients sequences were compared with that of the control sequence. Furthermore it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. Thus CTLA4 gene may not be responsible for an autoimmune disease SLE.
Abstract: Formaldehyde is the illegal chemical substance used
for food preservation in fish and vegetable. It can promote
carcinogenesis. Superoxide dismutases are the important
antioxidative enzymes that catalyze the dismutation of superoxide
anion into oxygen and hydrogen peroxide. The resultant level of
oxidative stress in formaldehyde-treated lymphocytes was
investigated. The formaldehyde concentrations of 0, 20, 40, 60, 80
and 120μmol/L were treated in human lymphocytes for 12 hours.
After 12 treated hours, the superoxide dismutase activity change was
measured in formaldehyde-treated lymphocytes. The results showed
that the formaldehyde concentrations of 60, 80 and 120μmol/L
significantly decreased superoxide dismutase activities in
lymphocytes (P < 0.05). The change of superoxide dismutase
activity in formaldehyde-treated lymphocytes may be the biomarker
for detect cellular injury, such as damage to DNA, due to
formaldehyde exposure.
Abstract: In process control applications, above 90% of the
controllers are of PID type. This paper proposed a robust PI
controller with fractional-order integrator. The PI parameters were
obtained using classical Ziegler-Nichols rules but enhanced with the
application of error filter cascaded to the fractional-order PI. The
controller was applied on steam temperature process that was
described by FOPDT transfer function. The process can be classified
as lag dominating process with very small relative dead-time. The
proposed control scheme was compared with other PI controller
tuned using Ziegler-Nichols and AMIGO rules. Other PI controller
with fractional-order integrator known as F-MIGO was also
considered. All the controllers were subjected to set point change and
load disturbance tests. The performance was measured using Integral
of Squared Error (ISE) and Integral of Control Signal (ICO). The
proposed controller produced best performance for all the tests with
the least ISE index.
Abstract: This is a genetic comparison study of Arabian Oryx
(Oryx leucoryx) population at two different locations (A &B) based
on nuclear microsatellite DNA markers. Arabian Oryx is listed as
vulnerable and endanger by the World Conservation Union (IUCN).
Thirty microsatellite markers from bovine family were applied to
investigate the genetic diversity of the Arabian Oryx and to set up a
molecular inventory. Among 30 microsatellite markers used, 13
markers were moderately polymorphic. Arabian Oryx at location A
has shown better gene diversity over location B. However, mean
number of alleles were less than location B. Data of within
population inbreeding coefficient indicates inbreeding at both
locations (A&B). Based on the analysis of polymorphic microsatellite
markers, the study revealed that Arabian Oryx need a genetically
designed breeding program.
Abstract: Atrazine, a herbicide widely used in sugarcane and corn production, is a frequently detected groundwater contaminant. An atrazine-degrading bacterium, strain KB02, was obtained from long-term atrazine-treated sugarcane field soils in Kanchanaburi province of Thailand. Strain KB02 had a rod-to-coccus morphological cycle during growth. Sequence analysis of the PCR product indicated that the 16S rRNA gene in strain KB02 was ranging from 97-98% identical to the same region in Klebsiella sp. Based on biochemical, physiological analysis and 16S rDNA sequence analysis of one representative isolate, strain KB02, the isolates belong to the genus Klebsiella in the family Enterobacteriaceae. Interestingly that the various primers for atzA, B and C failed to amplify genomic DNA of strain KB02. Whereas the expected PCR product of atzA, B and C were obtained from the reference strain, Arthrobacter sp. strain KU001.
Abstract: The identification and classification of weeds are of
major technical and economical importance in the agricultural
industry. To automate these activities, like in shape, color and
texture, weed control system is feasible. The goal of this paper is to
build a real-time, machine vision weed control system that can detect
weed locations. In order to accomplish this objective, a real-time
robotic system is developed to identify and locate outdoor plants
using machine vision technology and pattern recognition. The
algorithm is developed to classify images into broad and narrow class
for real-time selective herbicide application. The developed
algorithm has been tested on weeds at various locations, which have
shown that the algorithm to be very effectiveness in weed
identification. Further the results show a very reliable performance
on weeds under varying field conditions. The analysis of the results
shows over 90 percent classification accuracy over 140 sample
images (broad and narrow) with 70 samples from each category of
weeds.
Abstract: This paper investigates the performance of Multiple- Input Multiple-Output (MIMO) feedback system combined with Orthogonal Frequency Division Multiplexing (OFDM). Two types of codebook based channel feedback techniques are used in this work. The first feedback technique uses a combination of both the long-term and short-term channel state information (CSI) at the transmitter, whereas the second technique uses only the short term CSI. The long-term and short-term CSI at the transmitter is used for efficient channel utilization. OFDM is a powerful technique employed in communication systems suffering from frequency selectivity. Combined with multiple antennas at the transmitter and receiver, OFDM proves to be robust against delay spread. Moreover, it leads to significant data rates with improved bit error performance over links having only a single antenna at both the transmitter and receiver. The effectiveness of these techniques has been demonstrated through the simulation of a MIMO-OFDM feedback system. The results have been evaluated for 4x4 MIMO channels. Simulation results indicate the benefits of the MIMO-OFDM channel feedback system over the one without incorporating OFDM. Performance gain of about 3 dB is observed for MIMO-OFDM feedback system as compared to the one without employing OFDM. Hence MIMO-OFDM becomes an attractive approach for future high speed wireless communication systems.
Abstract: This paper will provide the kinematic and dynamic
analysis of a lower limb exoskeleton. The forward and inverse
kinematics of proposed exoskeleton is performed using Denevit and
Hartenberg method. The torques required for the actuators will be
calculated using Lagrangian formulation technique. This research can
be used to design the control of the proposed exoskeleton.
Abstract: Many digital signal processing, techniques have been used to automatically distinguish protein coding regions (exons) from non-coding regions (introns) in DNA sequences. In this work, we have characterized these sequences according to their nonlinear dynamical features such as moment invariants, correlation dimension, and largest Lyapunov exponent estimates. We have applied our model to a number of real sequences encoded into a time series using EIIP sequence indicators. In order to discriminate between coding and non coding DNA regions, the phase space trajectory was first reconstructed for coding and non-coding regions. Nonlinear dynamical features are extracted from those regions and used to investigate a difference between them. Our results indicate that the nonlinear dynamical characteristics have yielded significant differences between coding (CR) and non-coding regions (NCR) in DNA sequences. Finally, the classifier is tested on real genes where coding and non-coding regions are well known.
Abstract: We demonstrate a nonfaradaic electrochemical impedance spectroscopy measurement of biochemically modified gold plated electrodes using a two-electrode system. The absence of any redox indicator in the impedance measurements provide more precise and accurate characterization of the measured bioanalyte at molecular resolution. An equivalent electrical circuit of the electrodeelectrolyte interface was deduced from the observed impedance data of saline solution at low and high concentrations. The detection of biomolecular interactions was fundamentally correlated to electrical double-layer variation at modified interface. The investigations were done using 20mer deoxyribonucleic acid (DNA) strands without any label. Surface modification was performed by creating mixed monolayer of the thiol-modified single-stranded DNA and a spacer thiol (mercaptohexanol) by a two-step self-assembly method. The results clearly distinguish between the noncomplementary and complementary hybridization of DNA, at low frequency region below several hundreds Hertz.
Abstract: The aim of this study was to estimate the frequency of
EBV infection in Hodgkin's lymphoma (HL) and non-Hodgkin's
lymphoma (NHL) occurring in Jordanian patients. A total of 55
patients with lymphoma were examined in this study. Of 55 patients,
30 and 25 were diagnosed as HL and NHL, respectively. The four
HL subtypes were observed with the majority of the cases exhibited
the mixed cellularity (MC) subtype followed by the nodular sclerosis
(NS). The high grade was found to be the commonest subtype of
NHL in our sample, followed by the low grade. The presence of EBV
virus was detected by immunostating for expression of latent
membrane protein-1 (LMP-1). The frequency of LMP-1 expression
occurred more frequent in patients with HL (60.0%) than in patients
with NHL (32.0%). The frequency of LMP-1 expression was also
higher in patients with MC subtype (61.11%) than those patients with
NS (28.57%). No age or gender difference in occurrence of EBV
infection was observed among patient with HL. By contrast, the
prevalence of EBV infection in NHL patients aged below 50 was
lower (16.66%) than in NHL patients aged 50 or above (46.15%). In
addition, EBV infection was more frequent in females with NHL
(38.46%) than in male with NHL (25%). In NHL cases, the
frequency of EBV infection in intermediate grade (60.0%) was high
when compared with frequency of low (25%) or high grades (25%).
In conclusion, analysis of LMP-1 expression indicates an important
role for this viral oncogene in the pathogenesis of EBV-associated
malignant lymphomas. These data also support the previous findings
that people with EBV may develop lymphoma and that efforts to
maintain low lymphoma should be considered for people with EBV
infection.
Abstract: In biological and biomedical research motif finding tools are important in locating regulatory elements in DNA sequences. There are many such motif finding tools available, which often yield position weight matrices and significance indicators. These indicators, p-values and E-values, describe the likelihood that a motif alignment is generated by the background process, and the expected number of occurrences of the motif in the data set, respectively. The various tools often estimate these indicators differently, making them not directly comparable. One approach for comparing motifs from different tools, is computing the E-value as the product of the p-value and the number of possible alignments in the data set. In this paper we explore the combinatorics of the motif alignment models OOPS, ZOOPS, and ANR, and propose a generic algorithm for computing the number of possible combinations accurately. We also show that using the wrong alignment model can give E-values that significantly diverge from their true values.
Abstract: The problem of bin-packing in two dimensions (2BP) consists in placing a given set of rectangular items in a minimum number of rectangular and identical containers, called bins. This article treats the case of objects with a free orientation of 90Ôùª. We propose an approach of resolution combining optimization by colony of ants (ACO) and the heuristic method IMA to resolve this NP-Hard problem.
Abstract: A number of competing methodologies have been developed
to identify genes and classify DNA sequences into coding
and non-coding sequences. This classification process is fundamental
in gene finding and gene annotation tools and is one of the most
challenging tasks in bioinformatics and computational biology. An
information theory measure based on mutual information has shown
good accuracy in classifying DNA sequences into coding and noncoding.
In this paper we describe a species independent iterative
approach that distinguishes coding from non-coding sequences using
the mutual information measure (MIM). A set of sixty prokaryotes is
used to extract universal training data. To facilitate comparisons with
the published results of other researchers, a test set of 51 bacterial
and archaeal genomes was used to evaluate MIM. These results
demonstrate that MIM produces superior results while remaining
species independent.
Abstract: Legionella pneumophila is involved in more than 95%
cases of severe atypical pneumonia. Infection is mainly by
inhalation the indoor aerosols through the water-coolant systems.
Because some Legionella strains may be viable but not culturable,
therefore, Taq polymerase, DNA amplification and semi-nested-PCR
were carried out to detect Legionella-specific 16S-rDNA sequence.
For this purpose, 1.5 litter of water samples from 77 water-coolant
system were collected from four different hospitals, two nursing
homes and one student hostel in Kerman city of Iran, each in a brand
new plastic bottle during summer season of 2006 (from April to
August). The samples were filtered in the sterile condition through
the Millipore Membrane Filter. DNA was extracted from membrane
and used for PCR to detect Legionella spp. The PCR product was
then subjected to semi-nested PCR for detection of L. pneumophila.
Out of 77 water samples that were tested by PCR, 30 (39%) were
positive for most species of Legionella. However, L. pneumophila
was detected from 14 (18.2%) water samples by semi-nested PCR.
From the above results it can be concluded that water coolant
systems of different hospitals and nursing homes in Kerman city of
Iran are highly contaminated with L. pneumophila spp. and pose
serious concern. So, we recommend avoiding such type of coolant
system in the hospitals and nursing homes.